├── .tt_biocontainer_skip ├── tool_collections ├── gops │ ├── utils │ │ └── __init__.py │ ├── cluster │ │ ├── macros.xml │ │ ├── operation_filter.py │ │ ├── gops_clusterFind.gif │ │ ├── gops_clusterMerge.gif │ │ └── .shed.yml │ ├── concat │ │ ├── macros.xml │ │ ├── operation_filter.py │ │ ├── gops_concatenate.gif │ │ ├── test-data │ │ │ └── 1.interval │ │ └── .shed.yml │ ├── join │ │ ├── macros.xml │ │ ├── operation_filter.py │ │ ├── gops_joinInner.gif │ │ ├── gops_joinFullOuter.gif │ │ ├── gops_joinLeftOuter.gif │ │ ├── gops_joinRightOuter.gif │ │ ├── gops_joinRecordsList.gif │ │ └── .shed.yml │ ├── merge │ │ ├── macros.xml │ │ ├── operation_filter.py │ │ ├── gops_merge.gif │ │ ├── test-data │ │ │ └── gops_merge_out2.bed │ │ └── .shed.yml │ ├── basecoverage │ │ ├── macros.xml │ │ ├── test-data │ │ │ ├── gops_basecoverage_out.txt │ │ │ └── gops_basecoverage_out2.txt │ │ └── gops_baseCoverage.gif │ ├── complement │ │ ├── macros.xml │ │ ├── operation_filter.py │ │ ├── gops_complement.gif │ │ └── test-data │ │ │ └── gops_complement_out2.bed │ ├── coverage │ │ ├── macros.xml │ │ ├── operation_filter.py │ │ └── test-data │ │ │ └── gops_bigint2.interval │ ├── get_flanks │ │ ├── macros.xml │ │ ├── flanks_ex1.gif │ │ └── flanks_ex2.gif │ ├── intersect │ │ ├── macros.xml │ │ ├── utils │ │ │ ├── odict.py │ │ │ ├── __init__.py │ │ │ └── gff_util.py │ │ ├── operation_filter.py │ │ ├── test-data │ │ │ ├── gops_intersect_no_strand_out.bed │ │ │ ├── 12.bed │ │ │ ├── gops_bigint2.interval │ │ │ └── gops_intersect_bigint_out.interval │ │ ├── gops_intersectOverlappingPieces.gif │ │ ├── gops_intersectOverlappingIntervals.gif │ │ └── .shed.yml │ ├── subtract │ │ ├── macros.xml │ │ ├── utils │ │ │ ├── odict.py │ │ │ ├── __init__.py │ │ │ └── gff_util.py │ │ ├── operation_filter.py │ │ ├── gops_subtractOverlappingPieces.gif │ │ ├── gops_subtractOverlappingIntervals.gif │ │ └── .shed.yml │ ├── flanking_features │ │ ├── macros.xml │ │ ├── utils │ │ │ ├── odict.py │ │ │ ├── __init__.py │ │ │ └── gff_util.py │ │ └── test-data │ │ │ └── 4_windows_3.bed │ ├── subtract_query │ │ ├── macros.xml │ │ └── test-data │ │ │ ├── subtract-query-1.dat │ │ │ ├── subtract-query-3.dat │ │ │ └── 2.txt │ └── tables_arithmetic_operations │ │ └── test-data │ │ ├── numericalTable1.tabular │ │ ├── table_division_result.tabular │ │ ├── table_subtraction_result.tabular │ │ ├── table_addition_result.tabular │ │ └── table_multiplication_result.tabular ├── taxonomy │ ├── kraken2tax │ │ ├── tool-data │ │ │ └── ncbi_taxonomy.loc.sample │ │ ├── test-data │ │ │ ├── kraken2tax.txt │ │ │ ├── ncbi_taxonomy.loc.test │ │ │ ├── kraken2tax-test1.txt │ │ │ └── tax_dir │ │ │ │ └── nodes.dmp │ │ ├── tool_data_table_conf.xml.sample │ │ └── tool_data_table_conf.xml.test │ ├── find_diag_hits │ │ ├── test-data │ │ │ └── find_diag_hits.tabular │ │ └── tool_dependencies.xml │ ├── gi2taxonomy │ │ ├── test-data │ │ │ └── taxonomy2gi-input.tabular │ │ └── tool_dependencies.xml │ ├── t2ps │ │ ├── t2ps.tgz │ │ ├── t2ps_ideal.png │ │ ├── t2ps_heatmap.png │ │ ├── t2ps_autoscale.png │ │ ├── t2ps_ideal_ssp.png │ │ ├── t2ps_node_label.png │ │ ├── t2ps_autoscale_tree.png │ │ ├── t2ps_missing_nodes.png │ │ └── tool_dependencies.xml │ ├── poisson2test │ │ ├── test-data │ │ │ ├── poisson2test1.tabular │ │ │ └── poisson2test1_out.tabular │ │ └── tool_dependencies.xml │ ├── lca_wrapper │ │ ├── test-data │ │ │ ├── lca_output2.taxonomy │ │ │ └── lca_output.taxonomy │ │ └── tool_dependencies.xml │ └── t2t_report │ │ ├── tool_dependencies.xml │ │ └── test-data │ │ └── t2t_report.tabular ├── vcftools │ ├── vcftools_slice │ │ ├── test-data │ │ │ └── regions.bed │ │ ├── tool_dependencies.xml │ │ └── .shed.yml │ ├── vcftools_isec │ │ ├── tool_dependencies.xml │ │ └── .shed.yml │ ├── vcftools_merge │ │ ├── tool_dependencies.xml │ │ └── .shed.yml │ ├── vcftools_subset │ │ ├── tool_dependencies.xml │ │ └── .shed.yml │ ├── vcftools_annotate │ │ ├── tool_dependencies.xml │ │ └── .shed.yml │ ├── vcftools_compare │ │ ├── tool_dependencies.xml │ │ └── .shed.yml │ └── vcftools_consensus │ │ ├── tool_data_table_conf.xml.sample │ │ └── .shed.yml └── hgv │ ├── hgv_hilbertvis │ ├── hilbertvis1.png │ ├── hilbertvis2.png │ ├── hilbertvisDiagram.png │ ├── test-data │ │ └── hvis_mkar_chr22.pdf │ └── tool_dependencies.xml │ └── snpfreq │ ├── test-data │ └── snpFreqInput.txt │ └── tool_dependencies.xml ├── tools ├── fasta_concatenate_by_species │ └── utils │ │ └── __init__.py ├── fastq_trimmer_by_quality │ └── test-data │ │ ├── empty_file.dat │ │ └── sanger_full_range_empty_reads.fastqsanger ├── ccat │ ├── test-data │ │ ├── genome_length_mm8_chr19.txt │ │ ├── ccat_configurations.loc │ │ └── config_TF.txt │ ├── .shed.yml │ ├── tool_data_table_conf.xml.sample │ └── tool_data_table_conf.xml.test ├── ctd_batch │ └── test-data │ │ └── ctdBatchInput.txt ├── count_gff_features │ └── test-data │ │ ├── count_gff_features_out1.txt │ │ └── count_gff_features_out2.txt ├── cummerbund_to_tabular │ └── test-data │ │ ├── cds_count.tabular │ │ ├── cds_fpkm.tabular │ │ ├── cds_diff.tabular │ │ ├── cds_rg.tabular │ │ ├── cuffdiff_out.sqlite │ │ ├── cds_exp_diff.tabular │ │ ├── read_groups.tabular │ │ └── run_info.tabular ├── fasta_compute_length │ ├── test-data │ │ ├── merged.tab │ │ ├── dbkeys.loc │ │ ├── merged.fa │ │ └── fasta_tool_compute_length_3.out │ └── tool_data_table_conf.xml.sample ├── bowtie_wrappers │ ├── test-data │ │ ├── indexes │ │ │ └── equCab2chrM │ │ │ │ ├── equCab2chrM.3.ebwt │ │ │ │ ├── equCab2chrM.1.ebwt │ │ │ │ ├── equCab2chrM.2.ebwt │ │ │ │ ├── equCab2chrM.4.ebwt │ │ │ │ ├── equCab2chrM.rev.1.ebwt │ │ │ │ └── equCab2chrM.rev.2.ebwt │ │ ├── bowtie_indices.loc │ │ └── bowtie_out11.txt │ ├── tool_data_table_conf.xml.sample │ └── tool_data_table_conf.xml.test ├── correlation │ ├── test-data │ │ ├── cor_out.txt │ │ └── cor.tabular │ ├── kendall.png │ ├── pearson.png │ ├── spearman.png │ ├── tool_dependencies.xml │ └── .shed.yml ├── express │ ├── test-data │ │ ├── eXpress_varcov_all_params.xprs │ │ ├── eXpress_hits.bam │ │ ├── eXpress_hits_all_params.bam │ │ ├── eXpress_results.xprs │ │ ├── eXpress_results_sam.xprs │ │ └── eXpress_results_all_params.xprs │ └── tool_dependencies.xml ├── tophat │ ├── test-data │ │ ├── tophat_out3d.bed │ │ ├── tophat_out3i.bed │ │ ├── tophat_out1h.bam │ │ ├── tophat_out2h.bam │ │ ├── tophat_out3h.bam │ │ ├── tophat_out4h.bam │ │ ├── tophat_out1j.bed │ │ ├── tophat_out2j.bed │ │ ├── tophat_out3j.bed │ │ └── tophat_out4j.bed │ └── tool_data_table_conf.xml.sample ├── tophat2 │ ├── test-data │ │ ├── tophat_out3d.bed │ │ ├── tophat_out3i.bed │ │ ├── bowtie2_indices.loc │ │ ├── tophat_out1h.bam │ │ ├── tophat_out2h.bam │ │ ├── tophat_out3h.bam │ │ ├── tophat_out4h.bam │ │ ├── bowtie2 │ │ │ ├── tophat_test.1.bt2 │ │ │ ├── tophat_test.2.bt2 │ │ │ ├── tophat_test.3.bt2 │ │ │ ├── tophat_test.4.bt2 │ │ │ ├── tophat_test.rev.1.bt2 │ │ │ └── tophat_test.rev.2.bt2 │ │ ├── tophat2_out1j.bed │ │ ├── tophat2_out2j.bed │ │ ├── tophat2_out3j.bed │ │ └── tophat2_out4j.bed │ ├── tool_data_table_conf.xml.test │ └── tool_data_table_conf.xml.sample ├── dgidb_annotator │ └── test-data │ │ └── in1.tabular ├── windowsplitter │ ├── test-data │ │ └── 4.bed │ └── .shed.yml ├── pileup_parser │ ├── test-data │ │ ├── pileup_parser.6col.40-3-yes-yes.pileup.out │ │ ├── pileup_parser.6col.20-3-yes-no.pileup.out │ │ └── pileup_parser.6col.20-3-yes-yes.pileup.out │ ├── pileup_parser_help1.png │ ├── pileup_parser_help2.png │ ├── pileup_parser_help3.png │ └── pileup_parser_help4.png ├── histogram │ ├── histogram2.png │ ├── test-data │ │ ├── histogram_out1.pdf │ │ └── histogram_in1.tabular │ └── .shed.yml ├── lastz_paired_reads │ ├── test-data │ │ ├── lastz_paired_input3.fasta │ │ └── lastz_paired_out1.sam │ ├── tool_dependencies.xml │ └── tool_data_table_conf.xml.sample ├── xy_plot │ ├── xy_example.jpg │ └── test-data │ │ ├── testoutput.png │ │ ├── XY_Plot_1_out.pdf │ │ └── 2.tabular ├── compute_q_values │ ├── Q_plots.png │ ├── p_hist.png │ ├── q_hist.png │ ├── test-data │ │ └── p_q_hists_Q_plots.pdf │ └── tool_dependencies.xml ├── cummerbund │ └── test-data │ │ ├── pca.png │ │ ├── maplot.png │ │ ├── boxplot.png │ │ ├── density.png │ │ ├── fpkmSCV.png │ │ ├── heatmap.png │ │ ├── scatter.png │ │ ├── volcano.png │ │ ├── dendrogram.png │ │ ├── dispersion.png │ │ ├── expressionplot.png │ │ ├── scatterMatrix.png │ │ ├── cuffdiff_out.sqlite │ │ └── expressionbarplot.png ├── scatterplot │ ├── scatterplot.png │ ├── test-data │ │ ├── scatterplot_out1.pdf │ │ └── scatterplot_in1.tabular │ ├── .shed.yml │ └── tool_dependencies.xml ├── dwt_ivc_all │ └── test-data │ │ └── out2.pdf ├── dwt_cor_avb_all │ ├── test-data │ │ └── out2.pdf │ ├── dwt_cor_aVb_all_1.png │ ├── dwt_cor_aVb_all_10.png │ ├── dwt_cor_aVb_all_2.png │ ├── dwt_cor_aVb_all_3.png │ ├── dwt_cor_aVb_all_4.png │ ├── dwt_cor_aVb_all_5.png │ ├── dwt_cor_aVb_all_6.png │ ├── dwt_cor_aVb_all_7.png │ ├── dwt_cor_aVb_all_8.png │ └── dwt_cor_aVb_all_9.png ├── dwt_var_perclass │ └── test-data │ │ └── out.pdf ├── hisat │ ├── test-data │ │ ├── hisat_output_1.bam │ │ └── hisat_output_2.bam │ ├── tool_dependencies.xml │ └── tool_data_table_conf.xml.sample ├── trimmer │ ├── test-data │ │ ├── trimmer_a_f_c2_s1_e2_i62.dat │ │ ├── trimmer_a_f_c0_s1_e13_i62.dat │ │ └── trimmer_tab_delimited.dat │ └── .shed.yml ├── sicer │ └── test-data │ │ ├── chipseq_input.bed.gz │ │ └── chipseq_enriched.bed.gz ├── blat_mapping │ ├── blat_mapping_example.png │ └── test-data │ │ ├── blat_mapping_test1.txt │ │ └── blat_mapping_test1.out ├── dwt_cor_ava_perclass │ ├── dwt_cor_aVa_1.png │ ├── dwt_cor_aVa_2.png │ ├── dwt_cor_aVa_3.png │ ├── dwt_cor_aVa_4.png │ ├── dwt_cor_aVa_5.png │ └── test-data │ │ └── out2.pdf ├── convert_solid_color2nuc │ └── dualcolorcode.png ├── linear_regression │ └── test-data │ │ ├── regr_out.pdf │ │ ├── regr_inp.tabular │ │ └── regr_out.tabular ├── cd_hit_dup │ ├── test-data │ │ ├── cd-hit-dup_out_chimera.chimeric_clusters.tabular │ │ ├── cd-hit-dup_out_chimera.dup_clusters.tabular │ │ └── cd-hit-dup_out.dup_clusters.tabular │ └── tool_dependencies.xml ├── draw_stacked_barplots │ ├── stacked_bars_plot.png │ ├── test-data │ │ ├── stacked_barplot.pdf │ │ └── categories_criteria.tabular │ └── tool_dependencies.xml ├── fasta_to_tabular │ └── test-data │ │ ├── 1.tabular │ │ ├── 2.tabular │ │ ├── fasta_to_tabular_out2.tabular │ │ └── 4.fasta ├── dwt_var_perfeature │ ├── test-data │ │ ├── dwt_var_out2.pdf │ │ └── dwt_var_out1.tabular │ └── .shed.yml ├── partialr_square │ └── test-data │ │ ├── partialR_result.tabular │ │ └── regr_inp.tabular ├── plot_from_lda │ ├── test-data │ │ └── plot_for_lda_output.pdf │ └── tool_dependencies.xml ├── principal_component_analysis │ └── test-data │ │ ├── 1.tabular │ │ ├── pca_out2.pdf │ │ ├── pca_out4.pdf │ │ └── pca_out6.pdf ├── short_reads_figure_score │ ├── short_reads_boxplot.png │ └── test-data │ │ ├── 454Score.png │ │ └── solexaScore.png ├── canonical_correlation_analysis │ └── test-data │ │ ├── 1.tabular │ │ └── cca_out2.pdf ├── fastqsolexa_to_fasta_qual │ └── test-data │ │ ├── fastqsolexa_to_fasta_qual_out2.fasta │ │ ├── fastqsolexa_to_fasta_qual_out4.fasta │ │ ├── 2.fastqsolexa │ │ ├── fastqsolexa_to_fasta_qual_out2.qualsolexa │ │ ├── fastqsolexa_to_fasta_qual_out4.qualsolexa │ │ └── 1.fastqsolexa ├── kernel_canonical_correlation_analysis │ └── test-data │ │ ├── 1.tabular │ │ └── 2.tabular ├── kernel_principal_component_analysis │ └── test-data │ │ ├── 1.tabular │ │ ├── kpca_out2.pdf │ │ └── pca_out2.pdf ├── logistic_regression_vif │ └── test-data │ │ └── 2.tabular ├── megablast_xml_parser │ ├── test-data │ │ └── megablast_xml_parser_test1.gz │ └── .shed.yml ├── generate_pc_lda_matrix │ ├── first_matrix_generator_example_file.png │ └── second_matrix_generator_example_file.png ├── fasta_filter_by_length │ ├── test-data │ │ ├── fasta_tool_filter_length_2.out │ │ └── 4.fasta │ └── .shed.yml ├── sam2interval │ ├── test-data │ │ ├── sam2interval_noprintAll.dat │ │ ├── sam_bioinf_example.sam │ │ └── sam2interval_printAll.dat │ └── .shed.yml ├── short_reads_figure_high_quality_length │ ├── test-data │ │ ├── 454_high_quality_hist.pdf │ │ └── solexa_high_quality_hist.pdf │ └── tool_dependencies.xml ├── rmap │ ├── tool_dependencies.xml │ ├── test-data │ │ └── rmap_wrapper_test1.bed │ └── .shed.yml ├── rmapq │ ├── tool_dependencies.xml │ ├── test-data │ │ └── rmapq_wrapper_test1.bed │ └── .shed.yml ├── mine │ ├── tool_dependencies.xml │ └── .shed.yml ├── change_case │ ├── test-data │ │ ├── changeCase_out1.tabular │ │ └── 1.txt │ └── .shed.yml ├── lda_analysis │ ├── tool_dependencies.xml │ └── .shed.yml ├── t_test_two_samples │ ├── tool_dependencies.xml │ ├── test-data │ │ ├── t_test_result3.text │ │ ├── t_test_result1.text │ │ ├── t_test_result5.text │ │ ├── t_test_result4.text │ │ ├── t_test_result2.text │ │ └── t_test_result6.text │ └── .shed.yml ├── rcve │ └── test-data │ │ └── rcve_out.dat ├── categorize_elements_satisfying_criteria │ └── test-data │ │ ├── categorized_elements.tabular │ │ └── categories.tabular ├── microsatellite_birthdeath │ └── test-data │ │ └── regVariation │ │ └── microsatellite │ │ ├── Galaxy17_unmasked_short.maf.gz │ │ └── Galaxy17_unmasked_results.txt ├── table_annovar │ ├── tool_data_table_conf.xml.sample │ ├── tool_dependencies.xml │ └── .shed.yml ├── multispecies_orthologous_microsats │ ├── test-data │ │ └── regVariation │ │ │ └── microsatellite │ │ │ ├── Galaxy17_masked_short.maf.gz │ │ │ └── Galaxy17_unmasked_short.maf.gz │ └── .shed.yml ├── maf_cpg_filter │ ├── tool_dependencies.xml │ └── .shed.yml ├── pileup_interval │ └── test-data │ │ ├── pileup_interval_out1.tabular │ │ └── pileup_interval_out2.tabular ├── microsats_alignment_level │ └── tool_dependencies.xml ├── vcf2pgsnp │ └── .shed.yml ├── vcf_filter │ └── .shed.yml ├── cut_columns │ └── .shed.yml ├── tabular_to_fasta │ └── .shed.yml ├── divide_pg_snp │ └── test-data │ │ ├── dividePgSnp_input.pgSnp │ │ └── dividePgSnp_output.txt ├── best_regression_subsets │ └── tool_dependencies.xml ├── merge_cols │ └── .shed.yml ├── vcf_annotate │ └── .shed.yml ├── convert_characters │ └── .shed.yml ├── show_tail │ └── .shed.yml ├── condense_characters │ └── .shed.yml ├── tophat_fusion_post │ ├── .shed.yml │ └── tool_data_table_conf.xml.sample ├── add_value │ └── .shed.yml ├── sam_bitwise_flag_filter │ └── .shed.yml ├── show_beginning │ └── .shed.yml ├── vcf_intersect │ └── .shed.yml ├── vcf_extract │ └── .shed.yml ├── pgsnp2gd_snp │ └── .shed.yml ├── getindels_2way │ ├── .shed.yml │ └── tool_dependencies.xml ├── remove_beginning │ └── .shed.yml ├── varscan_version_2 │ └── .shed.yml ├── blat_coverage_report │ └── .shed.yml ├── substitutions │ └── .shed.yml ├── quality_filter │ ├── tool_dependencies.xml │ └── .shed.yml ├── featurecounter │ └── tool_dependencies.xml ├── weightedaverage │ └── tool_dependencies.xml ├── getindelrates_3way │ └── tool_dependencies.xml ├── microsats_mutability │ └── tool_dependencies.xml ├── pearson_correlation │ └── .shed.yml ├── short_reads_trim_seq │ └── .shed.yml └── substitution_rates │ └── .shed.yml ├── macros └── test │ └── read_group_macros.xml ├── deprecated ├── tools │ ├── annotation_profiler │ │ ├── tool-data │ │ │ └── annotation_profiler_valid_builds.txt.sample │ │ ├── test-data │ │ │ └── 4.bed │ │ └── tool_dependencies.xml │ ├── bamleftalign │ │ ├── README.rst │ │ ├── .shed.yml │ │ ├── test-data │ │ │ ├── left-align-input.bam │ │ │ └── left-align-output.bam │ │ └── tool-data │ │ │ └── tool_data_table_conf.xml.sample │ ├── bwa_wrappers │ │ ├── README.rst │ │ ├── .shed.yml │ │ └── tool_dependencies.xml │ ├── macs │ │ ├── test-data │ │ │ ├── peakcalling_macs │ │ │ │ └── test2 │ │ │ │ │ ├── Galaxy_Test_Run_model.r.log │ │ │ │ │ └── Galaxy_Test_Run_model.pdf │ │ │ ├── chipseq_input.bed.gz │ │ │ └── chipseq_enriched.bed.gz │ │ └── tool_dependencies.xml │ ├── dna_filtering │ │ ├── README.rst │ │ ├── histogram2.png │ │ ├── test-data │ │ │ ├── histogram_out1.pdf │ │ │ └── histogram_in1.tabular │ │ ├── tool_dependencies.xml │ │ └── .shed.yml │ ├── sam_merge │ │ ├── README.rst │ │ ├── test-data │ │ │ ├── sam_merge_in1.bam │ │ │ ├── sam_merge_in2.bam │ │ │ ├── sam_merge_in3.bam │ │ │ ├── sam_merge_out1.bam │ │ │ └── sam_merge_out2.bam │ │ ├── tool_dependencies.xml │ │ └── .shed.yml │ ├── sam_pileup │ │ ├── test-data │ │ │ ├── sam_pileup_in1.bam │ │ │ ├── sam_to_bam_out1.bam │ │ │ └── sam_to_bam_out2.bam │ │ └── tool_data_table_conf.xml.sample │ ├── bowtie_color_wrappers │ │ ├── test-data │ │ │ ├── bowtie_out3_1.fastq │ │ │ ├── bowtie_out3_2.fastq │ │ │ ├── bowtie_in1.fastqcssanger │ │ │ ├── bowtie_in3.fastqcssanger │ │ │ ├── bowtie_in4.fastqcssanger │ │ │ ├── bowtie_out1.sam │ │ │ └── bowtie_out4.sam │ │ ├── tool_dependencies.xml │ │ └── tool_data_table_conf.xml.sample │ └── megablast_wrapper │ │ ├── tool_dependencies.xml │ │ └── tool_data_table_conf.xml.sample ├── tool_collections │ └── gatk │ │ ├── count_covariates │ │ ├── test-data │ │ │ ├── gatk │ │ │ │ ├── fake_phiX_variant_locations.bed │ │ │ │ └── gatk_indel_realigner │ │ │ │ │ └── gatk_indel_realigner_out_1.bam │ │ │ └── 1.bam │ │ ├── tool_dependencies.xml │ │ └── tool_data_table_conf.xml.sample │ │ ├── variant_filtration │ │ ├── test-data │ │ │ └── gatk │ │ │ │ ├── fake_phiX_variant_locations.bed │ │ │ │ └── gatk_variant_filtration │ │ │ │ └── gatk_variant_filtration_out_1.log.contains │ │ ├── tool_dependencies.xml │ │ └── tool_data_table_conf.xml.sample │ │ ├── indel_realigner │ │ ├── test-data │ │ │ ├── gatk │ │ │ │ ├── gatk_realigner_target_creator │ │ │ │ │ └── gatk_realigner_target_creator_out_1.gatk_interval │ │ │ │ ├── fake_phiX_reads_1.bam │ │ │ │ └── gatk_indel_realigner │ │ │ │ │ ├── gatk_indel_realigner_out_1.bam │ │ │ │ │ └── gatk_indel_realigner_out_1.log.contains │ │ │ └── 1.bam │ │ ├── tool_dependencies.xml │ │ └── tool_data_table_conf.xml.sample │ │ ├── variants_validate │ │ ├── test-data │ │ │ └── gatk │ │ │ │ └── gatk_validate_variants │ │ │ │ └── gatk_validate_variants_out_1.log.contains │ │ ├── tool_dependencies.xml │ │ ├── .shed.yml │ │ └── tool_data_table_conf.xml.sample │ │ ├── realigner_target_creator │ │ ├── test-data │ │ │ ├── gatk │ │ │ │ ├── gatk_realigner_target_creator │ │ │ │ │ ├── gatk_realigner_target_creator_out_1.gatk_interval │ │ │ │ │ └── gatk_realigner_target_creator_out_1.log.contains │ │ │ │ └── fake_phiX_reads_1.bam │ │ │ └── 1.bam │ │ └── tool_dependencies.xml │ │ ├── print_reads │ │ ├── test-data │ │ │ ├── 1.bam │ │ │ └── gatk │ │ │ │ └── gatk_table_recalibration │ │ │ │ └── gatk_table_recalibration_out_1.bam │ │ ├── tool_dependencies.xml │ │ └── tool_data_table_conf.xml.sample │ │ ├── depth_of_coverage │ │ ├── test-data │ │ │ ├── 1.bam │ │ │ └── gatk │ │ │ │ ├── gatk_table_recalibration │ │ │ │ └── gatk_table_recalibration_out_1.bam │ │ │ │ └── gatk_depth_of_coverage │ │ │ │ └── gatk_depth_of_coverage_out_1_output_summary_sample.tabular │ │ ├── tool_dependencies.xml │ │ └── tool_data_table_conf.xml.sample │ │ ├── unified_genotyper │ │ ├── test-data │ │ │ ├── 1.bam │ │ │ └── gatk │ │ │ │ ├── gatk_table_recalibration │ │ │ │ └── gatk_table_recalibration_out_1.bam │ │ │ │ └── gatk_unified_genotyper │ │ │ │ └── gatk_unified_genotyper_out_1.metrics │ │ └── tool_dependencies.xml │ │ ├── variant_annotator │ │ ├── test-data │ │ │ ├── 1.bam │ │ │ └── gatk │ │ │ │ ├── gatk_table_recalibration │ │ │ │ └── gatk_table_recalibration_out_1.bam │ │ │ │ └── gatk_variant_annotator │ │ │ │ └── gatk_variant_annotator_out_1.log.contains │ │ └── tool_dependencies.xml │ │ ├── table_recalibration │ │ ├── test-data │ │ │ ├── 1.bam │ │ │ └── gatk │ │ │ │ ├── gatk_indel_realigner │ │ │ │ └── gatk_indel_realigner_out_1.bam │ │ │ │ └── gatk_table_recalibration │ │ │ │ └── gatk_table_recalibration_out_1.bam │ │ ├── tool_dependencies.xml │ │ └── tool_data_table_conf.xml.sample │ │ ├── variant_combine │ │ ├── tool_dependencies.xml │ │ ├── test-data │ │ │ └── gatk │ │ │ │ └── gatk_variant_combine │ │ │ │ └── gatk_variant_combine_out_1.log.contains │ │ └── tool_data_table_conf.xml.sample │ │ ├── variant_eval │ │ ├── tool_dependencies.xml │ │ ├── test-data │ │ │ └── gatk │ │ │ │ └── gatk_variant_eval │ │ │ │ └── gatk_variant_eval_out_1.log.contains │ │ ├── tool_data_table_conf.xml.sample │ │ └── .shed.yml │ │ ├── variant_select │ │ ├── tool_dependencies.xml │ │ ├── test-data │ │ │ └── gatk │ │ │ │ └── gatk_variant_select │ │ │ │ └── gatk_variant_select_out_1.log.contains │ │ └── tool_data_table_conf.xml.sample │ │ ├── variant_recalibrator │ │ └── tool_dependencies.xml │ │ ├── variant_apply_recalibration │ │ └── tool_dependencies.xml │ │ └── analyze_covariates │ │ └── tool_dependencies.xml ├── README.md └── data_managers │ ├── data_manager_fetch_genome_all_fasta │ ├── test-data │ │ └── phiX174_as_anoGam1.data_manager_json │ ├── tool_data_table_conf.xml.sample │ └── .shed.yml │ ├── data_manager_bwa_index_builder │ ├── tool_dependencies.xml │ └── .shed.yml │ └── data_manager_hisat_index_builder │ └── tool_dependencies.xml ├── setup.cfg ├── suites ├── suite_bamtools_2_3_0 │ ├── repository_dependencies.xml │ └── .shed.yml ├── suite_gops_1_0 │ └── .shed.yml └── suite_vcflib_14_08 │ └── .shed.yaml ├── packages ├── package_readline_6_2 │ └── .shed.yml ├── package_fastqc_0_11_2 │ └── .shed.yml ├── package_ghostscript_9_10 │ └── .shed.yml ├── package_gatk_1_4 │ └── .shed.yml ├── package_velvet_1_2_10 │ └── .shed.yml ├── package_freebayes_0_9_14_8a407cf5f4 │ └── .shed.yml ├── package_numpy_1_7 │ └── .shed.yml ├── package_rpy_1_0_3 │ └── .shed.yml ├── package_sputnik_1_0 │ └── .shed.yml ├── package_cran_yacca_1_0 │ └── .shed.yml ├── package_picard_1_126_0 │ └── .shed.yml ├── package_picard_1_56_0 │ └── .shed.yml ├── package_bioc_qvalue_1_34_0 │ └── .shed.yml ├── package_cufflinks_2_2_1 │ └── .shed.yml ├── package_cran_kernlab_0_1_4 │ └── .shed.yml ├── package_libgtextutils_0_6 │ └── .shed.yml ├── package_bwa_0_5_9 │ └── .shed.yml ├── package_bwa_0_6_2 │ └── .shed.yml ├── package_fastx_toolkit_0_0_13 │ └── .shed.yml ├── package_galaxy_ops_1_0_0 │ └── .shed.yml ├── package_bioc_hilbertvis_1_18_0 │ └── .shed.yml ├── package_freebayes_0_9_18_0059bdf │ └── .shed.yml ├── package_freebayes_0_9_20_b040236 │ └── .shed.yml ├── package_cufflinks_2_1_1 │ └── .shed.yml ├── package_inputproto_2_2 │ └── .shed.yml ├── package_freebayes_0_9_6_9608597d │ └── .shed.yml ├── package_picard_1_136 │ └── .shed.yml ├── package_libxtrans_1_2_7 │ └── .shed.yml ├── package_xorg_macros_1_17_1 │ └── .shed.yml ├── README.md └── package_ccat_3_0 │ └── .shed.yml ├── datatypes └── emboss_datatypes │ └── .shed.yml └── .github └── workflows └── slash.yaml /.tt_biocontainer_skip: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tool_collections/gops/utils/__init__.py: -------------------------------------------------------------------------------- 1 | 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/tools/kernel_canonical_correlation_analysis/test-data/2.tabular: -------------------------------------------------------------------------------- 1 | 1 68 4.1 2 | 2 71 4.6 3 | 3 62 3.8 4 | 4 75 4.4 5 | 5 58 3.2 6 | 6 60 3.1 7 | 7 67 3.8 8 | 8 68 4.1 9 | 9 71 4.3 10 | 10 69 3.7 11 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/realigner_target_creator/test-data/1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tool_collections/gatk/realigner_target_creator/test-data/1.bam -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [flake8] 2 | ignore = D,E501,W503 3 | # For flake8-import-order 4 | # https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py 5 | import-order-style = smarkets 6 | -------------------------------------------------------------------------------- /tool_collections/gops/merge/test-data/gops_merge_out2.bed: -------------------------------------------------------------------------------- 1 | chrM 69 852 2 | chrM 1148 3703 3 | chrM 3848 4933 4 | chrM 5326 6938 5 | chrM 7009 7699 6 | chrM 7765 8607 7 | chrM 9875 11542 8 | chrM 12405 15288 9 | -------------------------------------------------------------------------------- /tool_collections/gops/subtract_query/test-data/subtract-query-3.dat: -------------------------------------------------------------------------------- 1 | chr1 147984545 147984630 2 | chr10 55251623 55253124 3 | chr1 148185136 148185276 4 | chr1 147962192 147962580 5 | chr1 148078400 148078582 6 | -------------------------------------------------------------------------------- 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files for details. Now they serve as a reference and archive. 4 | -------------------------------------------------------------------------------- /tools/sam2interval/test-data/sam2interval_noprintAll.dat: -------------------------------------------------------------------------------- 1 | #chrom start end strand read_name 2 | ref 6 22 + r001 3 | ref 8 19 + r002 4 | ref 8 14 + r003 5 | ref 15 40 + r004 6 | ref 28 33 - r003 7 | ref 36 45 - r001 8 | -------------------------------------------------------------------------------- /deprecated/tools/macs/test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tools/macs/test-data/peakcalling_macs/test2/Galaxy_Test_Run_model.pdf -------------------------------------------------------------------------------- /tools/short_reads_figure_high_quality_length/test-data/454_high_quality_hist.pdf: 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CHR1 4225 19670 2 | CHR10 6 8 3 | CHR1 24417 24420 4 | CHR6_HLA_HAP2 0 150 5 | CHR2 1 5 6 | CHR10 2 10 7 | CHR1 30 55 8 | CHRY 1 20 9 | CHR1 1225979 42287290 10 | CHR10 7 8 11 | -------------------------------------------------------------------------------- /tools/correlation/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/plot_from_lda/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/tools/bowtie_color_wrappers/test-data/bowtie_out3_1.fastq: -------------------------------------------------------------------------------- 1 | + 2 | + 3 | 4=,'&+2#88)%$)''-0(56% 4 | 6;:8/>6997<5 5 | @1278_2032_148/1 6 | @1278_2032_216/1 7 | T221320102201031010032022 8 | T311231031130211223011020 9 | -------------------------------------------------------------------------------- /tools/bowtie_wrappers/test-data/bowtie_out11.txt: -------------------------------------------------------------------------------- 1 | # reads processed: 18 2 | # reads with at least one reported alignment: 13 (72.22%) 3 | # reads that failed to align: 5 (27.78%) 4 | Reported 13 paired-end alignments to 1 output stream(s) 5 | -------------------------------------------------------------------------------- /tools/ccat/test-data/config_TF.txt: -------------------------------------------------------------------------------- 1 | fragmentSize 200 2 | slidingWinSize 300 3 | movingStep 10 4 | isStrandSensitiveMode 1 5 | minCount 3 6 | outputNum 100000 7 | randomSeed 123456 8 | minScore 5.0 9 | bootstrapPass 50 10 | -------------------------------------------------------------------------------- /tools/fastqsolexa_to_fasta_qual/test-data/fastqsolexa_to_fasta_qual_out4.fasta: -------------------------------------------------------------------------------- 1 | >HANNIBAL_1_FC302VTAAXX:2:1:228:167 2 | GAATTGATCAGGACATAGGACAACTGTAGGCACCAT 3 | >HANNIBAL_1_FC302VTAAXX:2:1:156:340 4 | GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG 5 | -------------------------------------------------------------------------------- /tools/lda_analysis/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/tools/bowtie_color_wrappers/test-data/bowtie_out3_2.fastq: -------------------------------------------------------------------------------- 1 | + 2 | + 3 | 9490<4=:<=;8;;@<6;0>699# 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/tophat/test-data/tophat_out1j.bed: -------------------------------------------------------------------------------- 1 | track name=junctions description="TopHat junctions" 2 | test_chromosome 180 400 JUNC00000001 23 + 180 400 255,0,0 2 70,50 0,170 3 | test_chromosome 350 550 JUNC00000002 24 + 350 550 255,0,0 2 50,50 0,150 4 | -------------------------------------------------------------------------------- /tools/tophat/test-data/tophat_out2j.bed: -------------------------------------------------------------------------------- 1 | track name=junctions description="TopHat junctions" 2 | test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171 3 | test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150 4 | -------------------------------------------------------------------------------- /tools/tophat/test-data/tophat_out3j.bed: -------------------------------------------------------------------------------- 1 | track name=junctions description="TopHat junctions" 2 | test_chromosome 180 400 JUNC00000001 23 + 180 400 255,0,0 2 70,50 0,170 3 | test_chromosome 350 550 JUNC00000002 24 + 350 550 255,0,0 2 50,50 0,150 4 | -------------------------------------------------------------------------------- /tools/tophat/test-data/tophat_out4j.bed: -------------------------------------------------------------------------------- 1 | track name=junctions description="TopHat junctions" 2 | test_chromosome 179 400 JUNC00000001 38 + 179 400 255,0,0 2 71,50 0,171 3 | test_chromosome 350 549 JUNC00000002 30 + 350 549 255,0,0 2 50,49 0,150 4 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/realigner_target_creator/test-data/gatk/fake_phiX_reads_1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tool_collections/gatk/realigner_target_creator/test-data/gatk/fake_phiX_reads_1.bam -------------------------------------------------------------------------------- /tool_collections/gops/complement/test-data/gops_complement_out2.bed: -------------------------------------------------------------------------------- 1 | chrM 0 69 2 | chrM 852 1148 3 | chrM 3703 3848 4 | chrM 4933 5326 5 | chrM 6938 7009 6 | chrM 7699 7765 7 | chrM 8607 9875 8 | chrM 11542 12405 9 | chrM 15288 536870912 10 | -------------------------------------------------------------------------------- /tool_collections/gops/tables_arithmetic_operations/test-data/numericalTable1.tabular: -------------------------------------------------------------------------------- 1 | 5 4 4 5 4 5 6 6 2 | 10 11 12 14 15 14 19 23 3 | 1 1 1 1 1 1 1 1 4 | 1 2 1 2 2 1 4 3 5 | 2 4 4 5 4 4 5 5 6 | 3 1 2 1 1 2 3 3 7 | 6 7 5 1 1 2 2 2 8 | 4 4 4 5 8 7 6 6 9 | -------------------------------------------------------------------------------- /tool_collections/gops/tables_arithmetic_operations/test-data/table_division_result.tabular: -------------------------------------------------------------------------------- 1 | 1 1 1 1 1 1 1 1 2 | 1 1 1 1 1 1 1 1 3 | 1 1 1 1 1 1 1 1 4 | 1 1 1 1 1 1 1 1 5 | 1 1 1 1 1 1 1 1 6 | 1 1 1 1 1 1 1 1 7 | 1 1 1 1 1 1 1 1 8 | 1 1 1 1 1 1 1 1 9 | -------------------------------------------------------------------------------- /tool_collections/gops/tables_arithmetic_operations/test-data/table_subtraction_result.tabular: -------------------------------------------------------------------------------- 1 | 0 0 0 0 0 0 0 0 2 | 0 0 0 0 0 0 0 0 3 | 0 0 0 0 0 0 0 0 4 | 0 0 0 0 0 0 0 0 5 | 0 0 0 0 0 0 0 0 6 | 0 0 0 0 0 0 0 0 7 | 0 0 0 0 0 0 0 0 8 | 0 0 0 0 0 0 0 0 9 | -------------------------------------------------------------------------------- /tools/draw_stacked_barplots/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/rcve/test-data/rcve_out.dat: -------------------------------------------------------------------------------- 1 | #Model R-sq RCVE_Terms RCVE_Value 2 | 2 3 4 0.3997 - - 3 | 3 4 0.3319 2 0.1697 4 | 2 4 0.2974 3 0.2561 5 | 2 3 0.3985 4 0.0031 6 | 4 0.1226 2 3 0.6934 7 | 3 0.2733 2 4 0.3164 8 | 2 0.2972 3 4 0.2564 9 | -------------------------------------------------------------------------------- /tools/tophat2/test-data/tophat2_out1j.bed: -------------------------------------------------------------------------------- 1 | track name=junctions description="TopHat junctions" 2 | test_chromosome 180 400 JUNC00000001 19 + 180 400 255,0,0 2 70,50 0,170 3 | test_chromosome 350 550 JUNC00000002 23 + 350 550 255,0,0 2 50,50 0,150 4 | -------------------------------------------------------------------------------- /tools/tophat2/test-data/tophat2_out2j.bed: -------------------------------------------------------------------------------- 1 | track name=junctions description="TopHat junctions" 2 | test_chromosome 179 400 JUNC00000001 37 + 179 400 255,0,0 2 71,50 0,171 3 | test_chromosome 350 550 JUNC00000002 37 + 350 550 255,0,0 2 50,50 0,150 4 | -------------------------------------------------------------------------------- /tools/tophat2/test-data/tophat2_out3j.bed: -------------------------------------------------------------------------------- 1 | track name=junctions description="TopHat junctions" 2 | test_chromosome 180 400 JUNC00000001 19 + 180 400 255,0,0 2 70,50 0,170 3 | test_chromosome 350 550 JUNC00000002 23 + 350 550 255,0,0 2 50,50 0,150 4 | -------------------------------------------------------------------------------- /tools/tophat2/test-data/tophat2_out4j.bed: -------------------------------------------------------------------------------- 1 | track name=junctions description="TopHat junctions" 2 | test_chromosome 177 400 JUNC00000001 44 + 177 400 255,0,0 2 73,50 0,173 3 | test_chromosome 350 550 JUNC00000002 42 + 350 550 255,0,0 2 50,50 0,150 4 | -------------------------------------------------------------------------------- /deprecated/tools/bwa_wrappers/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/gops/subtract_query/test-data/2.txt: -------------------------------------------------------------------------------- 1 | chr1 4225 19670 2 | chr10 6 8 3 | chr1 24417 24420 4 | chr6_hla_hap2 0 150 5 | chr2 1 5 6 | chr1 30 55 7 | chrY 1 20 8 | chr1 1225979 42287290 9 | -------------------------------------------------------------------------------- /tools/blat_mapping/test-data/blat_mapping_test1.txt: -------------------------------------------------------------------------------- 1 | 10 1 0 0 0 0 0 0 + seq1 10 1 10 chrI 15080483 9704438 9704448 1 10, 1, 9704438, ggtttttttt, ggtttttatt, 2 | 5 1 0 0 0 0 0 0 + seq2 5 1 5 chrII 15080483 9704440 9704445 1 5, 1, 9704440, ttttt, tttta, 3 | -------------------------------------------------------------------------------- /tools/lastz_paired_reads/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/tools/annotation_profiler/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/tools/sam_merge/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/categorize_elements_satisfying_criteria/test-data/categorized_elements.tabular: -------------------------------------------------------------------------------- 1 | 10bp 20bp 40bp 2 | Deletion_Hotspots 2 2 3 3 | Dna_Pol_Pause_Frameshift 1 4 4 4 | Indel_Hotspots 0 0 0 5 | Insertion_Hotspots 1 1 2 6 | Topoisomerase_Cleavage_Sites 2 3 4 7 | -------------------------------------------------------------------------------- /tools/microsatellite_birthdeath/test-data/regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/tools/microsatellite_birthdeath/test-data/regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz -------------------------------------------------------------------------------- /tools/rmap/test-data/rmap_wrapper_test1.bed: -------------------------------------------------------------------------------- 1 | phix 360 396 seq1 1 - 2 | phix 4188 4224 seq2 1 + 3 | phix 4908 4944 seq4 0 - 4 | phix 2811 2847 seq5 2 + 5 | phix 3847 3883 seq6 0 - 6 | phix 91 127 seq7 0 + 7 | phix 2302 2338 seq8 2 + 8 | phix 2448 2484 seq9 0 + 9 | -------------------------------------------------------------------------------- /deprecated/data_managers/data_manager_fetch_genome_all_fasta/test-data/phiX174_as_anoGam1.data_manager_json: -------------------------------------------------------------------------------- 1 | {"data_tables": {"all_fasta": [{"path": "anoGam1.fa", "dbkey": "anoGam1", "name": "A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1)", "value": "anoGam1"}]}} -------------------------------------------------------------------------------- /tools/fastqsolexa_to_fasta_qual/test-data/2.fastqsolexa: -------------------------------------------------------------------------------- 1 | @seq1 2 | GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT 3 | +seq1 4 | hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh 5 | @seq2 6 | GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG 7 | +seq2 8 | hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO -------------------------------------------------------------------------------- /tools/microsatellite_birthdeath/test-data/regVariation/microsatellite/Galaxy17_unmasked_results.txt: -------------------------------------------------------------------------------- 1 | hg18.chr22 16119035 16119047 AGGG 4 NA ,1:G>A +ponAbe2 hg18:GGGGGAGGGAGGG,ponAbe2:GAGGGAGGGAGGG,calJac1:GGGGAAGGGAGGG,panTro2:GGGGGAGGGAGGG,rheMac2:GGGGGAGGGAGGG 2 | -------------------------------------------------------------------------------- /tools/rmapq/test-data/rmapq_wrapper_test1.bed: -------------------------------------------------------------------------------- 1 | phix 360 396 seq1 1 - 2 | phix 4188 4224 seq2 1 + 3 | phix 4908 4944 seq4 0 - 4 | phix 2811 2847 seq5 2 + 5 | phix 3847 3883 seq6 0 - 6 | phix 91 127 seq7 0 + 7 | phix 2302 2338 seq8 2 + 8 | phix 2448 2484 seq9 0 + 9 | -------------------------------------------------------------------------------- /tools/table_annovar/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | value, dbkey, type, path 5 | 6 |
7 | -------------------------------------------------------------------------------- /deprecated/tools/bowtie_color_wrappers/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/tophat2/tool_data_table_conf.xml.test: -------------------------------------------------------------------------------- 1 | 2 | 3 | value, dbkey, name, path 4 | 5 |
6 | 7 | -------------------------------------------------------------------------------- /tool_collections/gops/tables_arithmetic_operations/test-data/table_addition_result.tabular: -------------------------------------------------------------------------------- 1 | 10 8 8 10 8 10 12 12 2 | 20 22 24 28 30 28 38 46 3 | 2 2 2 2 2 2 2 2 4 | 2 4 2 4 4 2 8 6 5 | 4 8 8 10 8 8 10 10 6 | 6 2 4 2 2 4 6 6 7 | 12 14 10 2 2 4 4 4 8 | 8 8 8 10 16 14 12 12 9 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/lca_wrapper/test-data/lca_output2.taxonomy: -------------------------------------------------------------------------------- 1 | read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n 1 2 3 4 2 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_isec/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_merge/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_slice/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_subset/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/express/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/multispecies_orthologous_microsats/test-data/regVariation/microsatellite/Galaxy17_masked_short.maf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/tools/multispecies_orthologous_microsats/test-data/regVariation/microsatellite/Galaxy17_masked_short.maf.gz -------------------------------------------------------------------------------- /deprecated/data_managers/data_manager_bwa_index_builder/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/data_managers/data_manager_hisat_index_builder/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_annotate/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_compare/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/multispecies_orthologous_microsats/test-data/regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/tools/multispecies_orthologous_microsats/test-data/regVariation/microsatellite/Galaxy17_unmasked_short.maf.gz -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_consensus/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | value, dbkey, name, path 4 | 5 |
6 | 7 | -------------------------------------------------------------------------------- /tools/fastq_trimmer_by_quality/test-data/sanger_full_range_empty_reads.fastqsanger: -------------------------------------------------------------------------------- 1 | @FAKE0001 Original version has PHRED scores from 0 to 93 inclusive (in that order) 2 | 3 | + 4 | 5 | @FAKE0002 Original version has PHRED scores from 93 to 0 inclusive (in that order) 6 | 7 | + 8 | 9 | -------------------------------------------------------------------------------- /tools/maf_cpg_filter/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/pileup_interval/test-data/pileup_interval_out1.tabular: -------------------------------------------------------------------------------- 1 | chr1 0 1 G 2 | chr1 4 5 A 3 | chr1 10 12 CG 4 | chr1 13 15 AT 5 | chr1 16 17 T 6 | chr1 2734 2735 C 7 | chrM 2735 2743 ttacactc 8 | chrM 2757 2759 tc 9 | chrM 10872 10884 CCCAATTGCCGG 10 | chrM 10895 10899 TAGC 11 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/indel_realigner/test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tool_collections/gatk/indel_realigner/test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam -------------------------------------------------------------------------------- /tools/change_case/test-data/1.txt: -------------------------------------------------------------------------------- 1 | chr1 4225 19670 2 | chr10 6 8 3 | chr1 24417 24420 4 | chr6_hla_hap2 0 150 5 | chr2 1 5 6 | chr10 2 10 7 | chr1 30 55 8 | chrY 1 20 9 | chr1 1225979 42287290 10 | chr10 7 8 11 | -------------------------------------------------------------------------------- /tools/microsats_alignment_level/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/table_annovar/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | $REPOSITORY_INSTALL_DIR 5 | 6 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/count_covariates/test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tool_collections/gatk/count_covariates/test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam -------------------------------------------------------------------------------- /suites/suite_bamtools_2_3_0/repository_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/t2ps/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/print_reads/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tool_collections/gatk/print_reads/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam 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-------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_select/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/gops/concat/test-data/1.interval: -------------------------------------------------------------------------------- 1 | chr1 4348187 4348589 3.70 4.90 2.55 0.24 0.46 2 | chr1 4488177 4488442 4.03 5.77 1.92 -0.67 0.81 3 | chr1 4774091 4774440 8.07 8.33 7.82 0.85 -0.40 4 | chr1 4800122 4800409 6.40 7.35 5.44 1.19 -0.42 5 | chr1 4878925 4879277 2.18 0.28 4.93 -0.96 1.24 6 | -------------------------------------------------------------------------------- /tool_collections/gops/tables_arithmetic_operations/test-data/table_multiplication_result.tabular: -------------------------------------------------------------------------------- 1 | 25 16 16 25 16 25 36 36 2 | 100 121 144 196 225 196 361 529 3 | 1 1 1 1 1 1 1 1 4 | 1 4 1 4 4 1 16 9 5 | 4 16 16 25 16 16 25 25 6 | 9 1 4 1 1 4 9 9 7 | 36 49 25 1 1 4 4 4 8 | 16 16 16 25 64 49 36 36 9 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/t2t_report/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/cd_hit_dup/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_filtration/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_recalibrator/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variants_validate/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/find_diag_hits/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/gi2taxonomy/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/lca_wrapper/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/poisson2test/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/depth_of_coverage/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tool_collections/gatk/depth_of_coverage/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/unified_genotyper/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tool_collections/gatk/unified_genotyper/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_annotator/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tool_collections/gatk/variant_annotator/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam -------------------------------------------------------------------------------- /packages/package_readline_6_2/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: rl62 4 | name: package_readline_6_2 5 | owner: devteam 6 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_readline_6_2 7 | type: tool_dependency_definition 8 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/kraken2tax/test-data/tax_dir/nodes.dmp: -------------------------------------------------------------------------------- 1 | 1 | 1 | no rank | | 8 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | | 2 | 2 | 2 | superkingdom | | 0 | 0 | 11 | 0 | 0 | 0 | 0 | 0 | | 3 | 6 | 6 | genus | | 0 | 1 | 11 | 1 | 0 | 1 | 0 | 0 | | 4 | 7 | 7 | species | AC | 0 | 1 | 11 | 1 | 0 | 1 | 1 | 0 | | 5 | -------------------------------------------------------------------------------- /tools/lastz_paired_reads/test-data/lastz_paired_out1.sam: -------------------------------------------------------------------------------- 1 | F2YP0BU02F2LFK 65 chr21 9749451 255 331H34M1I7M * 0 0 TATCCACTTGCAGATTCCACGAAAACAGTGTTTCAAAAACTG EEEEEE<787@AAA/../:25////50EGE@CCI::@@@III 2 | F2YP0BU02GASSR 65 chr21 41805812 255 193H26M * 0 0 ATCATTGTTGTCTCTCCTGGTGGCAG IIIIIIIIIIIIIIIIIIH???BDCI 3 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/table_recalibration/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/tools-devteam/HEAD/deprecated/tool_collections/gatk/table_recalibration/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_apply_recalibration/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /tools/cd_hit_dup/test-data/cd-hit-dup_out_chimera.dup_clusters.tabular: -------------------------------------------------------------------------------- 1 | >Cluster 0 2 | 0 449nt, >A... * 3 | 1 449nt, >A2... at 1:449:1:449/+/100.00% 4 | >Cluster 1 5 | 0 440nt, >B... * 6 | 1 440nt, >B2... at 1:440:1:440/+/100.00% 7 | >Cluster 2 8 | 0 465nt, >C... * 9 | >Cluster 3 10 | 0 450nt, >D... * 11 | -------------------------------------------------------------------------------- /tools/cummerbund_to_tabular/test-data/read_groups.tabular: -------------------------------------------------------------------------------- 1 | file condition replicate_num total_mass norm_mass internal_scale external_scale 2 | /tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_26.dat q1 0 192 222.823 1 1 3 | /tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_27.dat q2 0 261 222.823 1.02899 1 4 | -------------------------------------------------------------------------------- /tools/fastqsolexa_to_fasta_qual/test-data/fastqsolexa_to_fasta_qual_out2.qualsolexa: -------------------------------------------------------------------------------- 1 | >seq1 2 | 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 0 40 40 40 40 40 40 3 | >seq2 4 | 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 33 40 40 40 40 23 40 1 40 6 40 19 9 10 7 3 40 15 5 | -------------------------------------------------------------------------------- /tools/pileup_interval/test-data/pileup_interval_out2.tabular: -------------------------------------------------------------------------------- 1 | chr1 5016024 5016030 ctctgc 2 | chr1 12459317 12459331 ATCTACACACATCT 3 | chr1 49116113 49116121 GGTTTTGT 4 | chr1 126866554 126866555 C 5 | chr11 1021429 1021446 GTGACGTGGGCTGTGTC 6 | chr14 1021450 1021451 T 7 | chr14 80839358 80839371 TTCTGGATATTTA 8 | -------------------------------------------------------------------------------- /suites/suite_gops_1_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Genomic Interval Operations 3 | description: Installs full gops tool suite. 4 | name: suite_gops_1_0 5 | owner: devteam 6 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/suites/suite_gops_1_0 7 | type: repository_suite_definition 8 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/depth_of_coverage/test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular: -------------------------------------------------------------------------------- 1 | sample_id total mean granular_third_quartile granular_median granular_first_quartile %_bases_above_15 2 | A Fake phiX Sample 360 0.07 1 1 1 0.0 3 | Total 360 0.07 N/A N/A N/A 4 | -------------------------------------------------------------------------------- /packages/package_fastqc_0_11_2/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: fastqc v 0.11.2 4 | name: package_fastqc_0_11_2 5 | owner: devteam 6 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_fastqc_0_11_2 7 | type: tool_dependency_definition 8 | -------------------------------------------------------------------------------- /tools/vcf2pgsnp/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: VCF to pgSnp 4 | long_description: | 5 | Convert from VCF to pgSnp format 6 | name: vcf2pgsnp 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf2pgsnp 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /tools/blat_mapping/test-data/blat_mapping_test1.out: -------------------------------------------------------------------------------- 1 | variableStep chrom=chrI 2 | 9704438 1 3 | 9704439 1 4 | 9704440 1 5 | 9704441 1 6 | 9704442 1 7 | 9704443 1 8 | 9704444 1 9 | 9704445 1 10 | 9704446 1 11 | 9704447 1 12 | variableStep chrom=chrII 13 | 9704440 1 14 | 9704441 1 15 | 9704442 1 16 | 9704443 1 17 | 9704444 1 18 | -------------------------------------------------------------------------------- /tools/express/test-data/eXpress_results.xprs: -------------------------------------------------------------------------------- 1 | bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable 2 | 1 comp54169_c1_seq1 15308 8801.217623 23 23 23.000000 40.004010 0.000000 0.000000 113620.642380 0.000000 253208.274573 T 3 | -------------------------------------------------------------------------------- /tools/express/test-data/eXpress_results_sam.xprs: -------------------------------------------------------------------------------- 1 | bundle_id target_id length eff_length tot_counts uniq_counts est_counts eff_counts ambig_distr_alpha ambig_distr_beta fpkm fpkm_conf_low fpkm_conf_high solvable 2 | 1 comp54169_c1_seq1 15308 8801.217623 23 23 23.000000 40.004010 0.000000 0.000000 113620.642380 0.000000 253208.274573 T 3 | -------------------------------------------------------------------------------- /packages/package_ghostscript_9_10/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: package_ghostscript_9_10 4 | name: package_ghostscript_9_10 5 | owner: devteam 6 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_ghostscript_9_10 7 | type: tool_dependency_definition 8 | -------------------------------------------------------------------------------- /deprecated/tools/bowtie_color_wrappers/test-data/bowtie_in1.fastqcssanger: -------------------------------------------------------------------------------- 1 | @869_1532_1255/1 2 | G2102223311000312223321002 3 | + 4 | =;8:?@=?;;9:8;=>;5A?;<8>< 5 | @1278_2032_148/1 6 | T221320102201031010032022 7 | + 8 | 4=,'&+2#88)%$)''-0(56% 9 | @1278_2032_216/1 10 | T311231031130211223011020 11 | + 12 | 6;:8/>6997<5 13 | -------------------------------------------------------------------------------- /deprecated/tools/bowtie_color_wrappers/test-data/bowtie_in3.fastqcssanger: -------------------------------------------------------------------------------- 1 | @869_1532_1255/1 2 | G2102223311000312223321002 3 | + 4 | =;8:?@=?;;9:8;=>;5A?;<8>< 5 | @1278_2032_148/1 6 | T221320102201031010032022 7 | + 8 | 4=,'&+2#88)%$)''-0(56% 9 | @1278_2032_216/1 10 | T311231031130211223011020 11 | + 12 | 6;:8/>6997<5 13 | -------------------------------------------------------------------------------- /tools/correlation/test-data/cor.tabular: -------------------------------------------------------------------------------- 1 | Person Height Self Esteem 2 | 1 68 4.1 3 | 2 71 4.6 4 | 3 62 3.8 5 | 4 75 4.4 6 | 5 58 3.2 7 | 6 60 3.1 8 | 7 67 3.8 9 | 8 68 4.1 10 | 9 71 4.3 11 | 1 69 3.7 12 | 1 68 3.5 13 | 1 67 3.2 14 | 1 63 3.7 15 | 1 62 3.3 16 | 1 60 3.4 17 | 1 63 4.0 18 | 1 65 4.1 19 | 1 67 3.8 20 | 1 63 3.4 21 | 2 61 3.6 -------------------------------------------------------------------------------- /tools/vcf_filter/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Filter a VCF file 4 | long_description: | 5 | This tool uses vcfPytools' filter command 6 | name: vcf_filter 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_filter 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /deprecated/tools/bowtie_color_wrappers/test-data/bowtie_in4.fastqcssanger: -------------------------------------------------------------------------------- 1 | @869_1532_1255/2 2 | T1301222000112122113330022 3 | + 4 | ;89<:==5<8>69;8=<9;<>9:=< 5 | @1278_2031_2013/1 6 | G0200321200313231222033313 7 | + 8 | ;21)8/5#5;45,)945#2173#.92 9 | @1278_2032_148/2 10 | G0020213032312123000133222 11 | + 12 | 9490<4=:<=;8;;@<6;0>699#Cluster 0 2 | 0 465nt, >C... * 3 | >Cluster 1 4 | 0 450nt, >D... * 5 | >Cluster 2 6 | 0 449nt, >A... * 7 | 1 449nt, >A2... at 1:449:1:449/+/100.00% 8 | >Cluster 3 9 | 0 440nt, >B... * 10 | 1 440nt, >B2... at 1:440:1:440/+/100.00% 11 | >Cluster 4 12 | 0 440nt, >chimeric_read... * 13 | -------------------------------------------------------------------------------- /tools/sam2interval/test-data/sam_bioinf_example.sam: -------------------------------------------------------------------------------- 1 | r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * 2 | r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * 3 | r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 4 | r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC * 5 | r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 6 | r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * 7 | -------------------------------------------------------------------------------- /deprecated/data_managers/data_manager_fetch_genome_all_fasta/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | value, dbkey, name, path 5 | 6 |
7 | 8 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/indel_realigner/test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains: -------------------------------------------------------------------------------- 1 | GenomeAnalysisEngine - Strictness is SILENT 2 | TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 3 | TraversalEngine - Total runtime 4 | TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%) -------------------------------------------------------------------------------- /tool_collections/gops/concat/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Genomic Interval Operations 3 | description: Concatenate two bed files 4 | name: concat 5 | owner: devteam 6 | homepage_url: https://github.com/galaxyproject/gops 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/concat 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /tools/fasta_compute_length/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | value, dbkey, name, path 5 | 6 |
7 | 8 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/kraken2tax/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tools/bowtie_color_wrappers/test-data/bowtie_out1.sam: -------------------------------------------------------------------------------- 1 | 1278_2032_148/1 4 * 0 0 * * 0 0 GCTGACAGGACATCACAATGAGG ,'&+2#88)%$)''-0(56% XM:i:0 2 | 1278_2032_216/1 4 * 0 0 * * 0 0 CCGTCATCCTAGCCGGTACCAGA :8/>6997<5 XM:i:0 3 | 869_1532_1255/1 16 chrM 3753 255 23M * 0 0 TTTGATAGAGTAAAACATAGAGG YUSVY_UOXZWRQRSUY[\^XQ! XA:i:1 MD:Z:23 NM:i:0 CM:i:1 4 | -------------------------------------------------------------------------------- /tool_collections/gops/cluster/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Genomic Interval Operations 3 | description: Cluster the intervals of a dataset 4 | name: cluster 5 | owner: devteam 6 | homepage_url: https://github.com/galaxyproject/gops 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/cluster 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/lca_wrapper/test-data/lca_output.taxonomy: -------------------------------------------------------------------------------- 1 | read_1 1 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum1 subphylum1 superclass1 class1 subclass1 superorder1 order1 suborder1 superfamily1 family1 subfamily1 tribe1 subtribe1 n n n n 1 2 | read_2 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 n n n n n n n n n n n n n n n n n 1 3 | -------------------------------------------------------------------------------- /tools/fastqsolexa_to_fasta_qual/test-data/fastqsolexa_to_fasta_qual_out4.qualsolexa: -------------------------------------------------------------------------------- 1 | >HANNIBAL_1_FC302VTAAXX:2:1:228:167 2 | 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4 3 | >HANNIBAL_1_FC302VTAAXX:2:1:156:340 4 | 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9 5 | -------------------------------------------------------------------------------- /tools/rmap/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Next Gen Mappers 3 | description: RMAP for Solexa Short Reads Alignment 4 | long_description: | 5 | This tool runs rmap, mapping Solexa reads onto a genome build. 6 | name: rmap 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmap 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /deprecated/tools/bowtie_color_wrappers/test-data/bowtie_out4.sam: -------------------------------------------------------------------------------- 1 | 1278_2032_148/1 4 * 0 0 * * 0 0 GCTGACAGGACATCACAATGAGG ,'&+2#88)%$)''-0(56% XM:i:0 2 | 1278_2032_216/1 4 * 0 0 * * 0 0 CCGTCATCCTAGCCGGTACCAGA :8/>6997<5 XM:i:0 3 | 869_1532_1255/1 16 chrM 3752 255 25M * 0 0 CTTTGATAGAGTAAAACATAGAGGC 2 | 3 | 4 | 5 | value, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_subset/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Select samples from a VCF dataset 4 | name: vcftools_subset 5 | owner: devteam 6 | homepage_url: https://vcftools.github.io/ 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_subset 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /tools/cut_columns/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Select columns from a dataset. 4 | long_description: | 5 | This tool selects specific columns from the input dataset. 6 | name: cut_columns 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/cut_columns 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /tools/hisat/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/tabular_to_fasta/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Convert Formats 3 | description: Tabular-to-FASTA 4 | long_description: | 5 | Converts tab delimited data into FASTA formatted sequences. 6 | name: tabular_to_fasta 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/tabular_to_fasta 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/realigner_target_creator/test-data/gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains: -------------------------------------------------------------------------------- 1 | GenomeAnalysisEngine - Strictness is SILENT 2 | TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 3 | TraversalEngine - Total runtime 4 | TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%) -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_select/test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains: -------------------------------------------------------------------------------- 1 | GenomeAnalysisEngine - Strictness is SILENT 2 | SelectVariants - Including sample 'A Fake phiX Sample' 3 | TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining 4 | SelectVariants - 1 records processed. 5 | -------------------------------------------------------------------------------- /packages/package_gatk_1_4/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and installs version 4 | 1.4 of GATK. 5 | name: package_gatk_1_4 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_gatk_1_4 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /tool_collections/gops/intersect/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Genomic Interval Operations 3 | description: Intersect the intervals of two datasets 4 | name: intersect 5 | owner: devteam 6 | homepage_url: https://github.com/galaxyproject/gops 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_slice/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Subset VCF dataset by genomic regions 4 | name: vcftools_slice 5 | owner: devteam 6 | homepage_url: https://vcftools.github.io/ 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_slice 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /tools/divide_pg_snp/test-data/dividePgSnp_input.pgSnp: -------------------------------------------------------------------------------- 1 | chr1 256 257 A/C 2 4,5 0,0 2 | chr1 56100 56101 A 1 8 0 3 | chr1 77052 77053 A/G 2 3,5 0,0 4 | chr1 110904 110905 A 1 5 0 5 | chr1 160592 160593 G 1 3 0 6 | chr1 640353 640354 G 1 1 0 7 | chr1 695314 695315 A 1 7 0 8 | chr1 713681 713682 A 1 8 0 9 | chr1 713965 713966 A/G 2 3,2 0,0 10 | chr1 714056 714057 A/G 2 1,5 0,0 11 | -------------------------------------------------------------------------------- /tools/linear_regression/test-data/regr_out.tabular: -------------------------------------------------------------------------------- 1 | Y-intercept -28.1169126094 2 | p-value (Y-intercept) 0.2942632048 3 | Slope (c1) 5.7471341245 4 | p-value (c1) 0.001732877 5 | Slope (c2) 0.9042745374 6 | p-value (c2) 0.1146675468 7 | R-squared 0.93881 8 | Adjusted R-squared 0.92132 9 | F-statistic {'dendf': 7.0, 'value': '53.69463', 'numdf': 2.0} 10 | Sigma 7.4345007113 11 | -------------------------------------------------------------------------------- /deprecated/tools/dna_filtering/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/best_regression_subsets/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/short_reads_figure_high_quality_length/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/t_test_two_samples/test-data/t_test_result3.text: -------------------------------------------------------------------------------- 1 | 2 | Two Sample t-test 3 | 4 | data: sample1 and sample2 5 | t = -0.9174, df = 4344, p-value = 0.1795 6 | alternative hypothesis: true difference in means is less than 0 7 | 95 percent confidence interval: 8 | -Inf 0.002555295 9 | sample estimates: 10 | mean of x mean of y 11 | 0.01196503 0.01518638 12 | 13 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_merge/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Merge multiple VCF datasets into a single dataset 4 | name: vcftools_merge 5 | owner: devteam 6 | homepage_url: https://vcftools.github.io/ 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /tools/merge_cols/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Merge columns together. 4 | long_description: | 5 | This tool merges two or more columns from the input dataset into a single column. 6 | name: merge_cols 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /tools/t_test_two_samples/test-data/t_test_result1.text: -------------------------------------------------------------------------------- 1 | 2 | Two Sample t-test 3 | 4 | data: sample1 and sample2 5 | t = -0.9174, df = 4344, p-value = 0.3590 6 | alternative hypothesis: true difference in means is not equal to 0 7 | 95 percent confidence interval: 8 | -0.010105104 0.003662398 9 | sample estimates: 10 | mean of x mean of y 11 | 0.01196503 0.01518638 12 | 13 | -------------------------------------------------------------------------------- /tools/t_test_two_samples/test-data/t_test_result5.text: -------------------------------------------------------------------------------- 1 | 2 | Two Sample t-test 3 | 4 | data: sample1 and sample2 5 | t = -0.9174, df = 4344, p-value = 0.8205 6 | alternative hypothesis: true difference in means is greater than 0 7 | 95 percent confidence interval: 8 | -0.008998001 Inf 9 | sample estimates: 10 | mean of x mean of y 11 | 0.01196503 0.01518638 12 | 13 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_eval/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.log.contains: -------------------------------------------------------------------------------- 1 | HelpFormatter - Program Args: -T VariantEval 2 | GenomeAnalysisEngine - Strictness is SILENT 3 | TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining 4 | VariantEvalWalker - Finalizing variant report 5 | TraversalEngine - Total runtime -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_filtration/test-data/gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains: -------------------------------------------------------------------------------- 1 | GenomeAnalysisEngine - Strictness is SILENT 2 | TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 3 | TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining 4 | TraversalEngine - Total runtime 5 | -------------------------------------------------------------------------------- /tools/change_case/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Convert column case. 4 | long_description: | 5 | This tool takes the specified columns and converts them to uppercase 6 | or lowercase. 7 | name: change_case 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/change_case 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/divide_pg_snp/test-data/dividePgSnp_output.txt: -------------------------------------------------------------------------------- 1 | chr1 256 257 A 4 0 C 5 0 2 | chr1 56100 56101 A 8 0 N 0 0 3 | chr1 77052 77053 A 3 0 G 5 0 4 | chr1 110904 110905 A 5 0 N 0 0 5 | chr1 160592 160593 G 3 0 N 0 0 6 | chr1 640353 640354 G 1 0 N 0 0 7 | chr1 695314 695315 A 7 0 N 0 0 8 | chr1 713681 713682 A 8 0 N 0 0 9 | chr1 713965 713966 A 3 0 G 2 0 10 | chr1 714056 714057 A 1 0 G 5 0 11 | -------------------------------------------------------------------------------- /tools/t_test_two_samples/test-data/t_test_result4.text: -------------------------------------------------------------------------------- 1 | 2 | Welch Two Sample t-test 3 | 4 | data: sample1 and sample2 5 | t = -0.9174, df = 4285.304, p-value = 0.1795 6 | alternative hypothesis: true difference in means is less than 0 7 | 95 percent confidence interval: 8 | -Inf 0.002555312 9 | sample estimates: 10 | mean of x mean of y 11 | 0.01196503 0.01518638 12 | 13 | -------------------------------------------------------------------------------- /tools/vcf_annotate/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: 'Annotate a VCF file (dbSNP, hapmap)' 4 | long_description: | 5 | This tool uses vcfPytools'' annotate command to annotate a VCF file 6 | name: vcf_annotate 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_annotate 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /packages/package_velvet_1_2_10/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and installs version 4 | 1.2.10 of Velvet 5 | name: package_velvet_1_2_10 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_velvet_1_2_10 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /tool_collections/hgv/snpfreq/test-data/snpFreqInput.txt: -------------------------------------------------------------------------------- 1 | chr1 210 211 38 4 15 56 0 1 x 2 | chr1 215 216 53 0 4 5 0 51 x 3 | chr1 228 229 55 0 2 56 0 1 x 4 | chr1 230 231 46 0 11 55 0 2 x 5 | chr1 234 235 43 0 14 55 0 2 x 6 | chr1 236 237 55 0 2 13 10 34 x 7 | chr1 437 438 55 0 2 46 0 11 x 8 | chr1 439 440 56 0 1 55 0 2 x 9 | chr1 449 450 56 0 1 13 20 24 x 10 | chr1 518 519 56 0 1 38 4 15 x 11 | -------------------------------------------------------------------------------- /tool_collections/hgv/snpfreq/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_annotate/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Annotate VCF using custom/user-defined annotations 4 | name: vcftools_annotate 5 | owner: devteam 6 | homepage_url: https://vcftools.github.io/ 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /tools/convert_characters/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Convert delimiters to tab. 4 | long_description: | 5 | Convert all delimiters of the selected type into TAB characters. 6 | name: convert_characters 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/convert_characters 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /tools/correlation/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Statistics 3 | description: Correlation for numeric columns 4 | long_description: | 5 | This tool computes the matrix of correlation coefficients between 6 | numeric columns. 7 | name: correlation 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/correlation 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/dwt_var_perfeature/test-data/dwt_var_out1.tabular: -------------------------------------------------------------------------------- 1 | Wavelet\ Variance\ Pvalue\ Test 2 | Scale\_1\ 129\ 0\ L 3 | Scale\_2\ 159\ 0\ L 4 | Scale\_4\ 223\ 0\ L 5 | Scale\_8\ 341\ 0\.0\d*\ L 6 | Scale\_16\ 381\ 0\.\d*\ L 7 | Scale\_32\ 753\ 0\.00\d*\ R 8 | Scale\_64\ 5746\ 0\ R 9 | Scale\_128\ 21985\ 0\ R 10 | Scale\_256\ 18580\ 0\ R 11 | Scale\_512\ 61815\ 0\ R 12 | Scale\_1024\ 65206\ 0\ R 13 | -------------------------------------------------------------------------------- /tools/show_tail/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Select lines from the end of a file. 4 | long_description: | 5 | This tool outputs the specified number of lines from the end of the input dataset. 6 | name: show_tail 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_tail 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /tools/t_test_two_samples/test-data/t_test_result2.text: -------------------------------------------------------------------------------- 1 | 2 | Welch Two Sample t-test 3 | 4 | data: sample1 and sample2 5 | t = -0.9174, df = 4285.304, p-value = 0.3590 6 | alternative hypothesis: true difference in means is not equal to 0 7 | 95 percent confidence interval: 8 | -0.010105130 0.003662424 9 | sample estimates: 10 | mean of x mean of y 11 | 0.01196503 0.01518638 12 | 13 | -------------------------------------------------------------------------------- /tools/t_test_two_samples/test-data/t_test_result6.text: -------------------------------------------------------------------------------- 1 | 2 | Welch Two Sample t-test 3 | 4 | data: sample1 and sample2 5 | t = -0.9174, df = 4285.304, p-value = 0.8205 6 | alternative hypothesis: true difference in means is greater than 0 7 | 95 percent confidence interval: 8 | -0.008998018 Inf 9 | sample estimates: 10 | mean of x mean of y 11 | 0.01196503 0.01518638 12 | 13 | -------------------------------------------------------------------------------- /packages/package_freebayes_0_9_14_8a407cf5f4/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Variant Analysis 4 | description: Dependencies for FreeBayes and LeftAlign wrappers 5 | name: freebayes_0_9_14_8a407cf5f4 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_freebayes_0_9_14_8a407cf5f4 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_numpy_1_7/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 1.7 of the the python numpy package 5 | name: package_numpy_1_7 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_numpy_1_7 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_rpy_1_0_3/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and installs version 4 | 1.0.3 of the python R interface. 5 | name: package_rpy_1_0_3 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_rpy_1_0_3 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_sputnik_1_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and installs version 4 | 1.0 of the Sputnik package. 5 | name: package_sputnik_1_0 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_sputnik_1_0 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_compare/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Compare VCF files to get overlap and uniqueness statistics 4 | name: vcftools_compare 5 | owner: devteam 6 | homepage_url: https://vcftools.github.io/ 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /tools/rmapq/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Next Gen Mappers 3 | description: RMAPQ for Solexa Short Reads Alignment with Quality Scores 4 | long_description: | 5 | This tool runs rmapq, searching against a genome build with sequence qualities. 6 | name: rmapq 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/rmapq 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/analyze_covariates/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /deprecated/tools/sam_pileup/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | value, dbkey, name, path 5 | 6 |
7 | 8 | -------------------------------------------------------------------------------- /tools/condense_characters/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Condense consecutive characters. 4 | long_description: | 5 | This tool condenses consecutive characters of the selected type. 6 | name: condense_characters 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/condense_characters 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /tools/fasta_filter_by_length/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Fasta Manipulation 3 | description: Filter sequences by length 4 | long_description: | 5 | Outputs sequences between Minimal length and Maximum length. 6 | name: fasta_filter_by_length 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_filter_by_length 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /tools/tophat_fusion_post/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Transcriptomics 3 | description: Wrapper for Tophat-Fusion post step 4 | long_description: | 5 | Plese see http://tophat.cbcb.umd.edu/fusion_index.html for details. 6 | name: tophat_fusion_post 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat_fusion_post 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /packages/package_cran_yacca_1_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and installs version 4 | 1.0 of the yacca R library. 5 | name: package_cran_yacca_1_0 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_cran_yacca_1_0 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_picard_1_126_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 1.126.0 of the Picard package. 5 | name: package_picard_1_126_0 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_picard_1_126_0 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_picard_1_56_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 1.56.0 of the Picard package. 5 | name: package_picard_1_56_0 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_picard_1_56_0 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/poisson2test/test-data/poisson2test1_out.tabular: -------------------------------------------------------------------------------- 1 | Acinetobacter 37 7 2.109 2.315 0.017468 0.010302 0.087342 0.051510 2 | Acyrthosiphon 70 21 1.549 1.612 0.060722 0.053481 0.303609 0.267406 3 | aedes 61 13 2.425 2.625 0.007645 0.004329 0.038223 0.021643 4 | Aeromonas 169 0 8.623 14.372 0.000000 0.000000 0.000000 0.000000 5 | anopheles 145 97 -3.217 -3.102 0.000647 0.000960 0.003234 0.004801 6 | -------------------------------------------------------------------------------- /tool_collections/vcftools/vcftools_consensus/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Apply VCF variants to a fasta file to create consensus sequence 4 | name: vcftools_consensus 5 | owner: devteam 6 | homepage_url: https://vcftools.github.io/ 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /tools/add_value/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Add a value as a new column. 4 | long_description: | 5 | This tool will take the given value and add it as a new column 6 | to every row of the input dataset. 7 | name: add_value 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/add_value 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/sam_bitwise_flag_filter/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - SAM 3 | description: Filter SAM on bitwise flag values 4 | long_description: | 5 | Allows parsing of SAM datasets using bitwise flag (the second column). 6 | name: sam_bitwise_flag_filter 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_bitwise_flag_filter 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /deprecated/tools/megablast_wrapper/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tool_collections/hgv/hgv_hilbertvis/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/table_recalibration/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /packages/package_bioc_qvalue_1_34_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and builds the Bioconductor 4 | qvalue R library. 5 | name: package_bioc_qvalue_1_34_0 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_bioc_qvalue_1_34_0 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_cufflinks_2_2_1/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 2.2.1 of the cufflinks RNA-Seq suite. 5 | name: package_cufflinks_2_2_1 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_cufflinks_2_2_1 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /tools/show_beginning/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Select lines from the beginning of a file. 4 | long_description: | 5 | This tool outputs the specified number of lines from the beginning of the input dataset. 6 | name: show_beginning 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/show_beginning 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /tools/vcf_intersect/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Generate the intersection of two VCF files 4 | long_description: | 5 | This tool uses vcfPytools' intersect command to generate the intersection of two VCF files 6 | name: vcf_intersect 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_intersect 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /deprecated/data_managers/data_manager_fetch_genome_all_fasta/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Data Managers 3 | description: Retrieve a FASTA file and populate the all_fasta.loc data table. 4 | long_description: '' 5 | name: data_manager_fetch_genome_all_fasta 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_fetch_genome_all_fasta 8 | type: unrestricted 9 | -------------------------------------------------------------------------------- /packages/package_cran_kernlab_0_1_4/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and installs version 4 | 0.1-4 of the kernlab R library. 5 | name: package_cran_kernlab_0_1_4 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_cran_kernlab_0_1_4 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_libgtextutils_0_6/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 0.6 of the gtextutils libraries. 5 | name: package_libgtextutils_0_6 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_libgtextutils_0_6 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /tools/vcf_extract/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Extract reads from a specified region 4 | long_description: | 5 | This tool uses vcfPytools'' extract command to extract reads from 6 | a specified region of a VCF file 7 | name: vcf_extract 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/vcf_extract 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_combine/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.log.contains: -------------------------------------------------------------------------------- 1 | HelpFormatter - Program Args: -T CombineVariants 2 | GenomeAnalysisEngine - Strictness is SILENT 3 | TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 4 | TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining 5 | TraversalEngine - Total runtime 6 | -------------------------------------------------------------------------------- /packages/package_bwa_0_5_9/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Tool Dependency Packages 4 | description: Contains a tool dependency definition that downloads and compiles version 5 | 0.5.9-r16 of the BWA package 6 | name: package_bwa_0_5_9 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_bwa_0_5_9 9 | type: tool_dependency_definition 10 | -------------------------------------------------------------------------------- /packages/package_bwa_0_6_2/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Tool Dependency Packages 4 | description: Contains a tool dependency definition that downloads and compiles version 5 | 0.6.2-r126 of the BWA package 6 | name: package_bwa_0_6_2 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_bwa_0_6_2 9 | type: tool_dependency_definition 10 | -------------------------------------------------------------------------------- /packages/package_fastx_toolkit_0_0_13/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 0.0.13 of the fastx toolkit. 5 | name: package_fastx_toolkit_0_0_13 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_fastx_toolkit_0_0_13 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_galaxy_ops_1_0_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 1.0 of the galaxy operations python package. 5 | name: package_galaxy_ops_1_0_0 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_galaxy_ops_1_0_0 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /tools/pgsnp2gd_snp/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Convert from pgSnp to gd_snp 4 | long_description: | 5 | This tool converts a pgSnp dataset to gd_snp format, either starting 6 | a new dataset or appending to an old one. 7 | name: pgsnp2gd_snp 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/pgsnp2gd_snp 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /packages/package_bioc_hilbertvis_1_18_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and builds the Bioconductor 4 | HilbertVis R library. 5 | name: package_bioc_hilbertvis_1_18_0 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_bioc_hilbertvis_1_18_0 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /tools/getindels_2way/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Variant Analysis 4 | description: Fetch Indels from pairwise alignments 5 | long_description: | 6 | This tool estimates the number of indels for every alignment block of the MAF file. 7 | name: getindels_2way 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/remove_beginning/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Remove lines from the beginning of a file. 4 | long_description: | 5 | This tool removes the specified number of lines from the beginning 6 | of the input dataset. 7 | name: remove_beginning 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/remove_beginning 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/trimmer/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Text Manipulation 3 | description: Trim leading or trailing characters. 4 | long_description: | 5 | Remove the specified number of characters from the beginning or 6 | end of each line or a single column in the input dataset. 7 | name: trimmer 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/trimmer 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/varscan_version_2/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: VarScan wrapper 4 | homepage_url: https://dkoboldt.github.io/varscan/ 5 | long_description: | 6 | VarScan is a variant caller for high-throughput sequencing data. 7 | name: varscan_version_2 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/varscan_version_2 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variants_validate/.shed.yml: -------------------------------------------------------------------------------- 1 | homepage_url: https://www.broadinstitute.org/gatk/ 2 | categories: 3 | - Variant Analysis 4 | description: Validate Variants 5 | long_description: | 6 | Validates a variants file. 7 | name: variants_validate 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gatk/variants_validate 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /packages/package_freebayes_0_9_18_0059bdf/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 0.9.18 (0059bdf) of FreeBayes. 5 | name: package_freebayes_0_9_18_0059bdf 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_freebayes_0_9_18_0059bdf 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_freebayes_0_9_20_b040236/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 0.9.20 (b040236) of FreeBayes. 5 | name: package_freebayes_0_9_20_b040236 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_freebayes_0_9_20_b040236 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /tools/fasta_compute_length/test-data/merged.fa: -------------------------------------------------------------------------------- 1 | >asdf length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ 2 | CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA 3 | >bsdf length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ 4 | CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG 5 | GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC 6 | CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC 7 | ATTGGTC 8 | -------------------------------------------------------------------------------- /deprecated/tools/macs/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/blat_coverage_report/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Next Gen Mappers 3 | - Sequence Analysis 4 | description: Polymorphism of the Reads 5 | long_description: | 6 | Calculate the percentage of reads supporting each nucleotide at 7 | each location 8 | name: blat_coverage_report 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /tools/scatterplot/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Graphics 3 | - Statistics 4 | description: Scatterplot of two numeric columns 5 | long_description: | 6 | This tool creates a simple scatter plot between two variables containing 7 | numeric values of a selected dataset. 8 | name: scatterplot 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /tools/t_test_two_samples/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Statistics 3 | description: T Test for Two Samples 4 | long_description: | 5 | This program implements the non-pooled t-test for two samples where 6 | the alternative hypothesis is two-sided or one-sided. 7 | name: t_test_two_samples 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/t_test_two_samples 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /deprecated/tools/sam_merge/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - SAM 3 | description: Merge BAM Files 4 | long_description: | 5 | This tool uses the Picard merge command to merge any number of 6 | BAM files together into one BAM file while preserving the BAM metadata such as read groups 7 | name: sam_merge 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam_merge 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/fasta_to_tabular/test-data/fasta_to_tabular_out2.tabular: -------------------------------------------------------------------------------- 1 | EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA 2 | EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGGGGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGCCACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCCATTGGTC 3 | -------------------------------------------------------------------------------- /tools/maf_cpg_filter/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Variant Analysis 4 | description: Mask CpG/non-CpG sites from MAF file 5 | long_description: | 6 | This tool takes a MAF file as input and masks CpG sites in every alignment block of the MAF file. 7 | name: maf_cpg_filter 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/substitutions/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Variant Analysis 4 | description: Fetch substitutions from pairwise alignments 5 | long_description: | 6 | This tool takes a pairwise MAF file as input and fetches substitutions per alignment block. 7 | name: substitutions 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /datatypes/emboss_datatypes/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | description: Galaxy applicable data formats used by Emboss tools. 4 | long_description: | 5 | Galaxy applicable data formats used by Emboss tools. This repository 6 | contains no tools. 7 | name: emboss_datatypes 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/datatypes/emboss_datatypes 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /deprecated/data_managers/data_manager_bwa_index_builder/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Data Managers 3 | description: Index a FASTA file using the Burrows-Wheeler algorithm and populate the 4 | bwa_index.loc file. 5 | long_description: '' 6 | name: data_manager_bwa_index_builder 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_index_builder 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /deprecated/tools/megablast_wrapper/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /packages/package_cufflinks_2_1_1/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | - Transcriptomics 4 | description: Contains a tool dependency definition that downloads and compiles version 5 | 2.1.1 of the cufflinks RNA-Seq suite. 6 | name: package_cufflinks_2_1_1 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_cufflinks_2_1_1 9 | type: tool_dependency_definition 10 | -------------------------------------------------------------------------------- /tools/draw_stacked_barplots/test-data/categories_criteria.tabular: -------------------------------------------------------------------------------- 1 | 10bp 20bp 40bp 80bp 160bp 320bp 640bp 1280bp 2 | Deletion_Hotspots 2 3 4 4 5 6 7 7 3 | Dna_Pol_Pause/Frameshift_Hotspots 8 10 14 17 18 15 19 20 4 | Indel_Hotspots 1 1 1 2 1 0 0 0 5 | Insertion_Hotspots 0 0 1 2 2 2 2 5 6 | Topoisomerase_Cleavage_Sites 2 3 5 4 3 3 4 4 7 | Translin_Targets 0 0 2 2 3 3 3 2 8 | VDJ_Recombination_Signals 0 0 1 1 1 2 2 2 9 | X-like_Sites 4 4 4 5 6 7 7 10 10 | -------------------------------------------------------------------------------- /tools/fasta_to_tabular/test-data/4.fasta: -------------------------------------------------------------------------------- 1 | >EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ 2 | CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA 3 | >EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ 4 | CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG 5 | GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC 6 | CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC 7 | ATTGGTC 8 | -------------------------------------------------------------------------------- /tools/getindels_2way/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/hisat/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /tools/lastz_paired_reads/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /tools/quality_filter/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/sam2interval/test-data/sam2interval_printAll.dat: -------------------------------------------------------------------------------- 1 | #chrom start end strand read_name 2 | ref 6 22 + r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * 3 | ref 8 19 + r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * 4 | ref 8 14 + r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 5 | ref 15 40 + r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC * 6 | ref 28 33 - r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 7 | ref 36 45 - r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * 8 | -------------------------------------------------------------------------------- /tool_collections/taxonomy/t2t_report/test-data/t2t_report.tabular: -------------------------------------------------------------------------------- 1 | root root 5 2 | superkingdom Eukaryota 5 3 | kingdom Metazoa 5 4 | phylum Chordata 5 5 | subphylum Craniata 5 6 | superclass Gnathostomata 5 7 | class Mammalia 5 8 | superorder Euarchontoglires 4 9 | order Primates 4 10 | suborder Haplorrhini 3 11 | superfamily Hominoidea 3 12 | family Hominidae 3 13 | genus Homo 2 14 | species Homo sapiens 2 15 | subspecies Homo sapiens neanderthalensis 1 16 | -------------------------------------------------------------------------------- /tools/compute_q_values/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/fasta_filter_by_length/test-data/4.fasta: -------------------------------------------------------------------------------- 1 | >EYKX4VC01B65GS length=54 xy=0784_1754 region=1 run=R_2007_11_07_16_15_57_ 2 | CCGGTATCCGGGTGCCGTGATGAGCGCCACCGGAACGAATTCGACTATGCCGAA 3 | >EYKX4VC01BNCSP length=187 xy=0558_3831 region=1 run=R_2007_11_07_16_15_57_ 4 | CTTACCGGTCACCACCGTGCCTTCAGGATTGATCGCCAGATCGGTCGGTGCGTCAGGCGG 5 | GGTGACATCGCCCACCACGGTACTCACTGGCTGGCTCTGGTTCCCGGCGGCATCGGAGGC 6 | CACCACGTTGAGGGTATTCCCCTCGGTTTGTGGCTCGGTGAGAACCACGTTGTAGTCGCC 7 | ATTGGTC 8 | -------------------------------------------------------------------------------- /tools/tophat_fusion_post/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | value, dbkey, name, path 4 | 5 |
6 | 7 | value, dbkey, name, path 8 | 9 |
10 | -------------------------------------------------------------------------------- /tools/windowsplitter/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Variant Analysis 4 | description: Make windows 5 | long_description: | 6 | This tool splits the intervals in the input file into smaller intervals 7 | based on the specified window-size and window type. 8 | name: windowsplitter 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /packages/package_inputproto_2_2/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: X.org InputProto protocol headers. 4 | long_description: | 5 | Provides header files for compiling packages that implement the 6 | X input protocol. 7 | name: package_inputproto_2_2 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_inputproto_2_2 10 | type: tool_dependency_definition 11 | -------------------------------------------------------------------------------- /tools/bowtie_wrappers/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /tools/categorize_elements_satisfying_criteria/test-data/categories.tabular: -------------------------------------------------------------------------------- 1 | Deletion_Hotspots deletionHoptspot1 deletionHoptspot2 deletionHoptspot3 2 | Dna_Pol_Pause_Frameshift dnaPolPauseFrameshift1 dnaPolPauseFrameshift2 dnaPolPauseFrameshift3 dnaPolPauseFrameshift4 3 | Indel_Hotspots indelHotspot1 4 | Insertion_Hotspots insertionHotspot1 insertionHotspot2 5 | Topoisomerase_Cleavage_Sites topoisomeraseCleavageSite1 topoisomeraseCleavageSite2 topoisomeraseCleavageSite3 6 | -------------------------------------------------------------------------------- /tools/cummerbund_to_tabular/test-data/run_info.tabular: -------------------------------------------------------------------------------- 1 | param value 2 | cmd_line cuffdiff --no-update-check --FDR=0.05 --num-threads=1 --min-alignment-count=0 --library-norm-method=geometric --dispersion-method=pooled --labels q1,q2 /tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_25.dat /tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_26.dat /tmp/tmpP3BAPq/tmpDkU5ls/database/files/000/dataset_27.dat 3 | version 2.2.1 4 | SVN_revision 4237 5 | boost_version 104700 6 | -------------------------------------------------------------------------------- /tools/featurecounter/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/lda_analysis/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Graphics 3 | - Statistics 4 | description: Perform Linear Discriminant Analysis 5 | long_description: | 6 | This tool consists of the module to perform the Linear Discriminant 7 | Analysis as described in Carrel et al., 2006 (PMID: 17009873) 8 | name: lda_analysis 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/lda_analysis 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /tools/mine/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Maximal Information-based Nonparametric Exploration 4 | long_description: | 5 | Applies the Maximal Information-based Nonparametric Exploration strategy to an input dataset. 6 | See http://www.exploredata.net/ for more information. 7 | name: mine 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/mine 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/weightedaverage/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/getindelrates_3way/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/microsats_mutability/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /tools/pearson_correlation/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Statistics 3 | description: Pearson and apos Correlation between any two numeric columns 4 | long_description: | 5 | Computes Pearsons correlation coefficient between any two numerical 6 | columns. Column numbers start at 1. 7 | name: pearson_correlation 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/pearson_correlation 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/print_reads/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /packages/package_freebayes_0_9_6_9608597d/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 0.9.6 (9608597d12e127c847ae03aa03440ab63992fedf) of FreeBayes. 5 | name: package_freebayes_0_9_6_9608597d 6 | owner: devteam 7 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_freebayes_0_9_6_9608597d 8 | type: tool_dependency_definition 9 | -------------------------------------------------------------------------------- /packages/package_picard_1_136/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 1.136 of the Picard package. 5 | homepage_url: http://broadinstitute.github.io/picard/ 6 | name: package_picard_1_136 7 | owner: devteam 8 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/blob/master/packages/package_picard_1_136/ 9 | type: tool_dependency_definition 10 | -------------------------------------------------------------------------------- /tools/bowtie_wrappers/tool_data_table_conf.xml.test: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /tools/ccat/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /tools/fasta_compute_length/test-data/fasta_tool_compute_length_3.out: -------------------------------------------------------------------------------- 1 | EYKX4VC01B65GS 54 2 | EYKX4VC01BNCSP 187 3 | EYKX4VC01CD9FT 115 4 | EYKX4VC01B8FW0 95 5 | EYKX4VC01BCGYW 115 6 | EYKX4VC01AZXC6 116 7 | EYKX4VC01CATH5 82 8 | EYKX4VC01BCEIV 47 9 | EYKX4VC01BWERM 83 10 | EYKX4VC01BT2O7 69 11 | EYKX4VC01BO0UO 222 12 | EYKX4VC01CBCPK 83 13 | EYKX4VC01B474S 54 14 | EYKX4VC01BB4QL 57 15 | EYKX4VC01BJ37M 64 16 | EYKX4VC01BV9R8 54 17 | EYKX4VC01CEPP8 60 18 | EYKX4VC01BTLME 78 19 | -------------------------------------------------------------------------------- /tools/tophat/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /.github/workflows/slash.yaml: -------------------------------------------------------------------------------- 1 | name: Slash Command Dispatch 2 | on: 3 | issue_comment: 4 | types: [created] 5 | jobs: 6 | slashCommandDispatch: 7 | runs-on: ubuntu-latest 8 | steps: 9 | - name: Slash Command Dispatch 10 | if: github.repository_owner == 'galaxyproject' 11 | uses: peter-evans/slash-command-dispatch@v5 12 | with: 13 | token: ${{ secrets.PAT }} 14 | commands: | 15 | run-all-tool-tests 16 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/count_covariates/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/depth_of_coverage/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/indel_realigner/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/unified_genotyper/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_annotator/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains: -------------------------------------------------------------------------------- 1 | GenomeAnalysisEngine - Strictness is SILENT 2 | TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 3 | TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining 4 | VariantAnnotator - Processed 1 loci. 5 | TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%) 6 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_annotator/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /deprecated/tools/bamleftalign/tool-data/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | line_type, value, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /packages/package_libxtrans_1_2_7/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Provides X Network Transport layer shared code. 4 | long_description: | 5 | Downloads and installs version 1.2.7 of the X Network Transport 6 | layer shared code. 7 | name: package_libxtrans_1_2_7 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_libxtrans_1_2_7 10 | type: tool_dependency_definition 11 | -------------------------------------------------------------------------------- /packages/package_xorg_macros_1_17_1/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: X.org macros utilities. 4 | long_description: | 5 | This package contains the aclocal macros needed for building xorg 6 | modules from upstream source. 7 | name: package_xorg_macros_1_17_1 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_xorg_macros_1_17_1 10 | type: tool_dependency_definition 11 | -------------------------------------------------------------------------------- /tools/short_reads_trim_seq/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Fastq Manipulation 3 | description: Select high quality segments 4 | long_description: | 5 | This tool finds high quality segments within sequencing reads generated 6 | by by Roche (454), Illumina (Solexa), or ABI SOLiD machines. 7 | name: short_reads_trim_seq 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_trim_seq 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/tophat2/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /tool_collections/gops/coverage/test-data/gops_bigint2.interval: -------------------------------------------------------------------------------- 1 | chrM 69 852 uc009vev.1_exon_0_0_chrM_70_f 0 + 2 | chrM 1148 3703 uc009vew.1_exon_0_0_chrM_1149_f 0 + 3 | chrM 3848 4933 uc009vex.1_exon_0_0_chrM_3849_f 0 + 4 | chrM 5326 6938 uc009vey.1_exon_0_0_chrM_5327_f 0 + 5 | chrM 7009 7699 uc009vez.1_exon_0_0_chrM_7010_f 0 + 6 | chrM 7765 8607 uc009vfa.1_exon_0_0_chrM_7766_f 0 + 7 | chrM 9875 11542 uc009vfb.1_exon_0_0_chrM_9876_f 0 + 8 | chrM 12405 15288 uc009vfc.1_exon_0_0_chrM_12406_f 0 + -------------------------------------------------------------------------------- /tool_collections/gops/intersect/test-data/gops_bigint2.interval: -------------------------------------------------------------------------------- 1 | chrM 69 852 uc009vev.1_exon_0_0_chrM_70_f 0 + 2 | chrM 1148 3703 uc009vew.1_exon_0_0_chrM_1149_f 0 + 3 | chrM 3848 4933 uc009vex.1_exon_0_0_chrM_3849_f 0 + 4 | chrM 5326 6938 uc009vey.1_exon_0_0_chrM_5327_f 0 + 5 | chrM 7009 7699 uc009vez.1_exon_0_0_chrM_7010_f 0 + 6 | chrM 7765 8607 uc009vfa.1_exon_0_0_chrM_7766_f 0 + 7 | chrM 9875 11542 uc009vfb.1_exon_0_0_chrM_9876_f 0 + 8 | chrM 12405 15288 uc009vfc.1_exon_0_0_chrM_12406_f 0 + -------------------------------------------------------------------------------- /tools/ccat/tool_data_table_conf.xml.test: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /tools/multispecies_orthologous_microsats/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Variant Analysis 4 | description: Extract orthologous microsatellites 5 | long_description: | 6 | This tool finds ortholgous microsatellite blocks between aligned species. 7 | name: multispecies_orthologous_microsats 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/sam2interval/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - SAM 3 | description: Convert SAM to interval. 4 | long_description: | 5 | Converts positional information from a SAM dataset into interval 6 | format with 0-based start and 1-based end. CIGAR string of SAM format is used to 7 | compute the end coordinate. 8 | name: sam2interval 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/sam2interval 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /tools/table_annovar/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: 'Annotate a VCF file using ANNOVAR annotations to produce a tabular file that can be filtered' 4 | long_description: | 5 | Please see the http://www.openbioinformatics.org/annovar/annovar_accessary.html#excel for details. 6 | name: table_annovar 7 | owner: devteam 8 | remote_repository_url: Nonehttps://github.com/galaxyproject/tools-devteam/tree/master/tools/table_annovar 9 | type: unrestricted 10 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/realigner_target_creator/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | -------------------------------------------------------------------------------- /suites/suite_bamtools_2_3_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | description: Contains tools for manipulating bamfiles. 4 | long_description: | 5 | BAMTools is a collection of utilities for manipulating BAM files. 6 | name: suite_bamtools_2_3_0 7 | owner: devteam 8 | homepage_url: https://github.com/pezmaster31/bamtools 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/suites/suite_bamtools_2_3_0 10 | type: repository_suite_definition 11 | -------------------------------------------------------------------------------- /tools/dwt_var_perfeature/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Statistics 3 | description: Wavelet variance using Discrete Wavelet Transfoms 4 | long_description: | 5 | This tool computes the scale-specific variance in wavelet coeffients 6 | obtained from the discrete wavelet transform of a feature of interest. 7 | name: dwt_var_perfeature 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/dwt_var_perfeature 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /tools/fastqsolexa_to_fasta_qual/test-data/1.fastqsolexa: -------------------------------------------------------------------------------- 1 | @HANNIBAL_1_FC302VTAAXX:2:1:228:167 2 | GAATTGATCAGGACATAGGACAACTGTAGGCACCAT 3 | +HANNIBAL_1_FC302VTAAXX:2:1:228:167 4 | 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4 5 | @HANNIBAL_1_FC302VTAAXX:2:1:156:340 6 | GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG 7 | +HANNIBAL_1_FC302VTAAXX:2:1:156:340 8 | 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9 -------------------------------------------------------------------------------- /tools/histogram/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Graphics 3 | - Statistics 4 | description: Histogram of a numeric column 5 | long_description: | 6 | This tool computes a histogram of the numerical values in a column of a dataset. 7 | name: histogram 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram 10 | homepage_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/unified_genotyper/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics: -------------------------------------------------------------------------------- 1 | Visited bases 5387 2 | Callable bases 5344 3 | Confidently called bases 5344 4 | % callable bases of all loci 99.202 5 | % confidently called bases of all loci 99.202 6 | % confidently called bases of callable loci 100.000 7 | Actual calls made 1 8 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/print_reads/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_eval/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tools/dna_filtering/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: Filter on ambiguities in polymorphism datasets 4 | long_description: | 5 | This tool is written for a very specific case related to an analysis 6 | of polymorphism data. Suppose you have a table of SNP data that looks like this:: 7 | name: dna_filtering 8 | owner: devteam 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/dna_filtering 10 | type: unrestricted 11 | -------------------------------------------------------------------------------- /suites/suite_vcflib_14_08/.shed.yaml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Variant Analysis 3 | description: A suite of Galaxy utilities associated with version 14.08 of the vcflib. 4 | long_description: | 5 | A simple C++ library for parsing and manipulating VCF files. 6 | name: suite_vcflib_14_08 7 | owner: devteam 8 | homepage_url: https://github.com/ekg/vcflib 9 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/suites/suite_vcflib_14_08 10 | type: repository_suite_definition 11 | -------------------------------------------------------------------------------- /tools/megablast_xml_parser/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Next Gen Mappers 3 | - Convert Formats 4 | description: Parse blast XML output 5 | long_description: | 6 | This tool processes the XML output of any NCBI blast tool (if you 7 | run your own blast jobs, the XML output can be generated with -m 7 option). 8 | name: megablast_xml_parser 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/megablast_xml_parser 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /tools/quality_filter/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Variant Analysis 4 | description: Filter nucleotides based on quality scores 5 | long_description: | 6 | This tool takes a MAF file as input and filters nucleotides in 7 | every alignment block of the MAF file based on their quality/PHRED scores. 8 | name: quality_filter 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /tools/substitution_rates/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Sequence Analysis 3 | - Variant Analysis 4 | description: Estimate substitution rates for non-coding regions 5 | long_description: | 6 | This tool takes a pairwise MAF file as input and estimates substitution 7 | rate according to Jukes-Cantor JC69 model. 8 | name: substitution_rates 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/count_covariates/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/depth_of_coverage/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/indel_realigner/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_combine/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_filtration/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_select/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variants_validate/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tools/bowtie_color_wrappers/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /tool_collections/gops/intersect/test-data/gops_intersect_bigint_out.interval: -------------------------------------------------------------------------------- 1 | chrM 69 852 uc009vev.1_exon_0_0_chrM_70_f 0 + 2 | chrM 1148 3703 uc009vew.1_exon_0_0_chrM_1149_f 0 + 3 | chrM 3848 4933 uc009vex.1_exon_0_0_chrM_3849_f 0 + 4 | chrM 5326 6938 uc009vey.1_exon_0_0_chrM_5327_f 0 + 5 | chrM 7009 7699 uc009vez.1_exon_0_0_chrM_7010_f 0 + 6 | chrM 7765 8607 uc009vfa.1_exon_0_0_chrM_7766_f 0 + 7 | chrM 9875 11542 uc009vfb.1_exon_0_0_chrM_9876_f 0 + 8 | chrM 12405 15288 uc009vfc.1_exon_0_0_chrM_12406_f 0 + 9 | -------------------------------------------------------------------------------- /tools/scatterplot/tool_dependencies.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/table_recalibration/tool_data_table_conf.xml.sample: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | value, dbkey, name, path 6 | 7 |
8 | 9 | -------------------------------------------------------------------------------- /deprecated/tool_collections/gatk/variant_eval/.shed.yml: -------------------------------------------------------------------------------- 1 | homepage_url: https://www.broadinstitute.org/gatk/ 2 | categories: 3 | - Variant Analysis 4 | description: Eval Variants 5 | long_description: | 6 | General-purpose tool for variant evaluation (% in dbSNP, genotype 7 | concordance, Ti/Tv ratios, and a lot more) 8 | name: variant_eval 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gatk/variant_eval 11 | type: unrestricted 12 | -------------------------------------------------------------------------------- /packages/README.md: -------------------------------------------------------------------------------- 1 | Historically Galaxy Tool Shed provided its own way of packaging software required for Galaxy tools. 2 | Some of the so called 'package recipes' are available in this folder and also available for installation 3 | at the Main Tool Shed. However Galaxy adopted the Conda package manager for such tasks and writing new 4 | package recipes is a deprecated activity. Read more about this transition and framework in 5 | our [documentation](https://docs.galaxyproject.org/en/master/admin/conda_faq.html). 6 | -------------------------------------------------------------------------------- /packages/package_ccat_3_0/.shed.yml: -------------------------------------------------------------------------------- 1 | categories: 2 | - Tool Dependency Packages 3 | description: Contains a tool dependency definition that downloads and compiles version 4 | 3.0 of CCAT. 5 | long_description: | 6 | CCAT is a software package for the analysis of ChIP-seq data with 7 | negative control. 8 | name: package_ccat_3_0 9 | owner: devteam 10 | remote_repository_url: https://github.com/galaxyproject/tools-devteam/tree/master/packages/package_ccat_3_0 11 | type: tool_dependency_definition 12 | --------------------------------------------------------------------------------