├── .coveragerc ├── .editorconfig ├── .git-blame-ignore-revs ├── .github ├── dependabot.yml └── workflows │ └── ci.yaml ├── .gitignore ├── .gitmodules ├── .isort.cfg ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── .travis.yml ├── CODE_OF_CONDUCT.rst ├── CONTRIBUTING.rst ├── HISTORY.rst ├── Jenkinsfile ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.rst ├── cwl-runner ├── README ├── cwl-runner └── setup.py ├── dev-requirements.txt ├── docs ├── .planemo.yml ├── Makefile ├── Vagrantfile ├── _running_external.rst ├── _running_intro.rst ├── _static │ └── .gitkeep ├── _writing_argparse.rst ├── _writing_clusters.rst ├── _writing_collections.rst ├── _writing_conclusion.rst ├── _writing_conda_fleeqtk.rst ├── _writing_conda_init.rst ├── _writing_conda_new.rst ├── _writing_conda_overview.rst ├── _writing_conda_recipe_complete.rst ├── _writing_conda_search.rst ├── _writing_containers_linter_explain.rst ├── _writing_containers_mulled_build.rst ├── _writing_containers_mulled_output.rst ├── _writing_containers_publishing.rst ├── _writing_cwl_intro.rst ├── _writing_dependencies_conda.rst ├── _writing_dependencies_conda_cwl.rst ├── _writing_dependencies_containers.rst ├── _writing_dependencies_containers_cwl.rst ├── _writing_from_help_command.rst ├── _writing_intro.rst ├── _writing_macros.rst ├── _writing_multiple_outputs.rst ├── _writing_parameters.rst ├── _writing_publish_intro.rst ├── _writing_scripts.rst ├── _writing_suites.rst ├── _writing_test_and_serve.rst ├── _writing_test_and_serve_appliance.rst ├── _writing_test_reports.rst ├── _writing_testing.rst ├── _writing_tool_metadata.rst ├── _writing_using_seqtk.rst ├── appliance.rst ├── automating_workflows.rst ├── autoupdate.rst ├── best_practices_workflows.rst ├── commands.rst ├── commands │ ├── autoupdate.rst │ ├── ci_find_repos.rst │ ├── ci_find_tools.rst │ ├── ci_setup.rst │ ├── clone.rst │ ├── conda_build.rst │ ├── conda_env.rst │ ├── conda_init.rst │ ├── conda_install.rst │ ├── conda_search.rst │ ├── config_init.rst │ ├── container_register.rst │ ├── create_alias.rst │ ├── database_create.rst │ ├── database_delete.rst │ ├── database_list.rst │ ├── delete_alias.rst │ ├── docker_build.rst │ ├── docker_shell.rst │ ├── dockstore_init.rst │ ├── docs.rst │ ├── lint.rst │ ├── list_alias.rst │ ├── list_invocations.rst │ ├── list_repos.rst │ ├── merge_test_reports.rst │ ├── mull.rst │ ├── mulled_init.rst │ ├── normalize.rst │ ├── open.rst │ ├── profile_create.rst │ ├── profile_delete.rst │ ├── profile_list.rst │ ├── project_init.rst │ ├── pull_request.rst │ ├── rerun.rst │ ├── run.rst │ ├── serve.rst │ ├── share_test.rst │ ├── shed_build.rst │ ├── shed_create.rst │ ├── shed_diff.rst │ ├── shed_init.rst │ ├── shed_lint.rst │ ├── shed_serve.rst │ ├── shed_test.rst │ ├── shed_update.rst │ ├── shed_upload.rst │ ├── syntax.rst │ ├── test.rst │ ├── test_reports.rst │ ├── tool_init.rst │ ├── training_fill_data_library.rst │ ├── training_generate_from_wf.rst │ ├── training_init.rst │ ├── upload_data.rst │ ├── virtualenv.rst │ ├── workflow_convert.rst │ ├── workflow_edit.rst │ ├── workflow_job_init.rst │ ├── workflow_lint.rst │ ├── workflow_test_init.rst │ ├── workflow_test_on_invocation.rst │ └── workflow_upload.rst ├── conduct.rst ├── conf.py ├── configuration.rst ├── contributing.rst ├── developing.rst ├── example_assertions.yml ├── example_travis_gxwf_docker.yml ├── example_travis_gxwf_native.yml ├── faqs.rst ├── galaxy_changelog.html ├── galaxy_changelog.md ├── history.rst ├── images │ ├── CWL-Logo-HD.png │ ├── dependency_resolution.png │ ├── gx_new_run_workflow.png │ ├── gx_new_workflow_editor.png │ ├── gx_subworkflow_example_brad_langhorst_neb.png │ ├── gx_toolbox_labels.png │ ├── gx_workflow_output_labels.png │ ├── identifiers.svg │ ├── kitematic_downloading.png │ ├── kitematic_exec.png │ ├── kitematic_root_prompt.png │ ├── kitematic_search.png │ ├── kitematic_ubuntu_prompt.png │ ├── mulledflow.png │ ├── nemo.gif │ ├── organic_mower_wat.jpg │ ├── ova_desktop.png │ ├── ova_icon.png │ ├── ova_import.png │ ├── ova_importing.png │ ├── ova_xubuntu_icon.png │ ├── seqtk_in_galaxy.png │ ├── subcollection_mapping_identifiers.svg │ ├── tool_test.png │ ├── workflow_best_practices.png │ └── workflow_outputs.png ├── index.rst ├── installation.rst ├── make.bat ├── modules.rst ├── notebooks │ ├── basics.ipynb │ └── cwl.ipynb ├── organization.rst ├── other_docs.rst ├── planemo.autopygen.commands.rst ├── planemo.autopygen.rst ├── planemo.autopygen.source_file_parsing.rst ├── planemo.autopygen.xml.rst ├── planemo.commands.rst ├── planemo.cwl.rst ├── planemo.database.rst ├── planemo.engine.rst ├── planemo.galaxy.rst ├── planemo.galaxy.test.rst ├── planemo.linters.rst ├── planemo.reports.rst ├── planemo.rst ├── planemo.shed.rst ├── planemo.shed2tap.rst ├── planemo.test.rst ├── planemo.training.rst ├── planemo.xml.rst ├── planemo_logo.png ├── posters │ └── planemo_workflow_sdk.odp ├── presentations │ ├── 2016_workflows.html │ ├── 2016_workflows.md │ ├── images │ └── style.css ├── publishing.rst ├── readme.rst ├── requirements.txt ├── run_galaxy_workflow_tests.sh ├── running.rst ├── test_example_collection_input.yml ├── test_example_composite_input.yml ├── test_example_nested_collection_input.yml ├── test_example_tagged_input.yml ├── test_format.rst ├── tests │ ├── tests_all.sh │ ├── tests_building.sh │ ├── tests_building_cwl.sh │ ├── tests_conda.sh │ ├── tests_conda_cwl.sh │ ├── tests_docker.sh │ ├── tests_docker_cwl.sh │ └── tests_tdd.sh ├── writing.rst ├── writing │ ├── bwa-mem_v1.xml │ ├── bwa-mem_v2.xml │ ├── bwa-mem_v3.xml │ ├── bwa-mem_v4.xml │ ├── bwa-mem_v5.xml │ ├── gc_content.pl │ ├── gc_content.xml │ ├── gen.sh │ ├── job_conf_slurm.xml │ ├── seqtk_macros.xml │ ├── seqtk_seq_v1.cwl │ ├── seqtk_seq_v1.xml │ ├── seqtk_seq_v2.cwl │ ├── seqtk_seq_v2.xml │ ├── seqtk_seq_v3.cwl │ ├── seqtk_seq_v3.xml │ ├── seqtk_seq_v3_job.yml │ ├── seqtk_seq_v3_tests.yml │ ├── seqtk_seq_v4.xml │ ├── seqtk_seq_v5.xml │ ├── seqtk_seq_v6.xml │ ├── seqtk_seq_with_macros.xml │ └── show_diffs.sh ├── writing_advanced.rst ├── writing_advanced_cwl.rst ├── writing_appliance.rst ├── writing_cwl.rst ├── writing_cwl_appliance.rst ├── writing_cwl_standalone.rst ├── writing_how_do_i.rst └── writing_standalone.rst ├── mypy.ini ├── planemo ├── __init__.py ├── autopygen │ ├── __init__.py │ ├── argument_parser_conversion.py │ ├── commands │ │ ├── __init__.py │ │ └── command_utils.py │ ├── param_info.py │ ├── source_file_parsing │ │ ├── __init__.py │ │ ├── constants.py │ │ ├── decoy_parser.py │ │ ├── local_module_parsing.py │ │ ├── parser_discovery_and_init.py │ │ ├── parsing_commons.py │ │ ├── parsing_exceptions.py │ │ └── unknown_names_discovery.py │ └── xml │ │ ├── __init__.py │ │ └── xml_utils.py ├── autoupdate.py ├── ci.py ├── cli.py ├── commands │ ├── __init__.py │ ├── cmd_autoupdate.py │ ├── cmd_ci_find_repos.py │ ├── cmd_ci_find_tools.py │ ├── cmd_ci_setup.py │ ├── cmd_clone.py │ ├── cmd_conda_build.py │ ├── cmd_conda_env.py │ ├── cmd_conda_init.py │ ├── cmd_conda_install.py │ ├── cmd_conda_search.py │ ├── cmd_config_init.py │ ├── cmd_container_register.py │ ├── cmd_create_alias.py │ ├── cmd_create_gist.py │ ├── cmd_database_create.py │ ├── cmd_database_delete.py │ ├── cmd_database_list.py │ ├── cmd_delete_alias.py │ ├── cmd_docker_build.py │ ├── cmd_docker_shell.py │ ├── cmd_dockstore_init.py │ ├── cmd_docs.py │ ├── cmd_invocation_download.py │ ├── cmd_invocation_export.py │ ├── cmd_job_config_init.py │ ├── cmd_lint.py │ ├── cmd_list_alias.py │ ├── cmd_list_invocations.py │ ├── cmd_list_repos.py │ ├── cmd_merge_test_reports.py │ ├── cmd_mull.py │ ├── cmd_mulled_init.py │ ├── cmd_normalize.py │ ├── cmd_open.py │ ├── cmd_profile_create.py │ ├── cmd_profile_delete.py │ ├── cmd_profile_job_config_init.py │ ├── cmd_profile_list.py │ ├── cmd_project_init.py │ ├── cmd_pull_request.py │ ├── cmd_rerun.py │ ├── cmd_run.py │ ├── cmd_serve.py │ ├── cmd_share_test.py │ ├── cmd_shed_build.py │ ├── cmd_shed_create.py │ ├── cmd_shed_diff.py │ ├── cmd_shed_download.py │ ├── cmd_shed_init.py │ ├── cmd_shed_lint.py │ ├── cmd_shed_serve.py │ ├── cmd_shed_test.py │ ├── cmd_shed_update.py │ ├── cmd_shed_upload.py │ ├── cmd_slurm_init.py │ ├── cmd_syntax.py │ ├── cmd_test.py │ ├── cmd_test_reports.py │ ├── cmd_tool_init.py │ ├── cmd_training_fill_data_library.py │ ├── cmd_training_generate_from_wf.py │ ├── cmd_training_init.py │ ├── cmd_upload_data.py │ ├── cmd_workflow_convert.py │ ├── cmd_workflow_edit.py │ ├── cmd_workflow_job_init.py │ ├── cmd_workflow_lint.py │ ├── cmd_workflow_test_init.py │ ├── cmd_workflow_test_on_invocation.py │ ├── cmd_workflow_track.py │ └── cmd_workflow_upload.py ├── conda.py ├── config.py ├── context.py ├── cwl │ ├── __init__.py │ ├── run.py │ └── toil.py ├── database │ ├── __init__.py │ ├── factory.py │ ├── interface.py │ ├── postgres.py │ ├── postgres_docker.py │ ├── postgres_singularity.py │ └── sqlite.py-wip ├── deps.py ├── docker.py ├── engine │ ├── __init__.py │ ├── cwltool.py │ ├── factory.py │ ├── galaxy.py │ ├── interface.py │ ├── test.py │ └── toil.py ├── exit_codes.py ├── galaxy │ ├── __init__.py │ ├── activity.py │ ├── api.py │ ├── config.py │ ├── distro_tools.py │ ├── ephemeris_sleep.py │ ├── invocations │ │ ├── __init__.py │ │ ├── api.py │ │ ├── polling.py │ │ ├── progress.py │ │ ├── progress_display.py │ │ └── simulations.py │ ├── profiles.py │ ├── run.py │ ├── serve.py │ ├── test │ │ ├── __init__.py │ │ ├── actions.py │ │ └── structures.py │ └── workflows.py ├── git.py ├── github_util.py ├── glob.py ├── io.py ├── lint.py ├── linters │ ├── __init__.py │ ├── biocontainer_registered.py │ ├── conda_requirements.py │ ├── doi.py │ ├── urls.py │ └── xsd.py ├── mulled.py ├── network_util.py ├── options.py ├── reports │ ├── __init__.py │ ├── allure.py │ ├── bootstrap.min.css │ ├── bootstrap.min.js │ ├── build_report.py │ ├── custom.css │ ├── custom.js │ ├── jquery.min.js │ ├── macros.tmpl │ ├── markdown-it.min.js │ ├── report_html.tpl │ ├── report_junit.tpl │ ├── report_markdown.tpl │ ├── report_markdown_minimal.tpl │ ├── report_text.tpl │ ├── report_xunit.tpl │ ├── xunit.tpl │ └── xunit_handler.py ├── runnable.py ├── runnable_resolve.py ├── scripts │ └── planemo-completion.sh ├── shed │ ├── __init__.py │ ├── diff.py │ └── interface.py ├── shed2tap │ ├── __init__.py │ └── base.py ├── shed_lint.py ├── templates.py ├── test │ ├── __init__.py │ ├── _check_output.py │ ├── data.py │ └── results.py ├── tool_builder.py ├── tool_lint.py ├── tools.py ├── training │ ├── __init__.py │ ├── tool_input.py │ ├── topic.py │ ├── tutorial.py │ └── utils.py ├── virtualenv.py ├── workflow_lint.py └── xml │ ├── __init__.py │ ├── diff.py │ ├── validation.py │ └── xsd │ ├── repository_dependencies.xsd │ └── tool_dependencies.xsd ├── project_templates ├── bwa │ ├── bwa-mem.xml │ └── test-data │ │ ├── bwa-aln-test1.bam │ │ ├── bwa-mem-fastq1.fq │ │ ├── bwa-mem-fastq2.fq │ │ └── bwa-mem-mt-genome.fa ├── conda_answers │ ├── exercise_1 │ │ ├── .shed.yml │ │ ├── pear.xml │ │ └── test-data │ │ │ ├── forward.fastq │ │ │ ├── pear_assembled_results1.fastq │ │ │ ├── pear_unassembled_forward_results1.fastq │ │ │ └── reverse.fastq │ └── exercise_2 │ │ ├── fleeqtk │ │ ├── build.sh │ │ └── meta.yaml │ │ ├── fleeqtk_seq.xml │ │ └── test-data │ │ ├── 2.fasta │ │ └── 2.fastq ├── conda_answers_cwl │ ├── exercise_1 │ │ ├── pear.cwl │ │ ├── pear_tests.yml │ │ └── test-data │ │ │ ├── forward.fastq │ │ │ ├── pear_assembled_results1.fastq │ │ │ ├── pear_unassembled_forward_results1.fastq │ │ │ └── reverse.fastq │ ├── exercise_2 │ │ ├── fleeqtk │ │ │ ├── build.sh │ │ │ └── meta.yaml │ │ ├── fleeqtk_seq.cwl │ │ ├── fleeqtk_seq_tests.yml │ │ └── test-data │ │ │ ├── 2.fasta │ │ │ └── 2.fastq │ └── exercise_3 │ │ ├── seqtk_seq.cwl │ │ ├── seqtk_seq_job.yml │ │ ├── seqtk_seq_tests.yml │ │ └── test-data │ │ ├── 2.fasta │ │ └── 2.fastq ├── conda_exercises │ ├── exercise_1 │ │ ├── .shed.yml │ │ ├── pear.xml │ │ └── test-data │ │ │ ├── forward.fastq │ │ │ ├── pear_assembled_results1.fastq │ │ │ ├── pear_unassembled_forward_results1.fastq │ │ │ └── reverse.fastq │ └── exercise_2 │ │ ├── fleeqtk_seq.xml │ │ └── test-data │ │ ├── 2.fasta │ │ └── 2.fastq ├── conda_exercises_cwl │ ├── exercise_1 │ │ ├── pear.cwl │ │ ├── pear_tests.yml │ │ └── test-data │ │ │ ├── forward.fastq │ │ │ ├── pear_assembled_results1.fastq │ │ │ ├── pear_unassembled_forward_results1.fastq │ │ │ └── reverse.fastq │ ├── exercise_2 │ │ ├── fleeqtk_seq.cwl │ │ ├── fleeqtk_seq_tests.yml │ │ └── test-data │ │ │ ├── 2.fasta │ │ │ └── 2.fastq │ └── exercise_3 │ │ ├── seqtk_seq.cwl │ │ ├── seqtk_seq_job.yml │ │ ├── seqtk_seq_tests.yml │ │ └── test-data │ │ ├── 2.fasta │ │ └── 2.fastq ├── conda_testing │ ├── bwa.xml │ └── bwa_and_samtools.xml ├── conda_testing_cwl │ ├── bwa_and_samtools.cwl │ └── bwa_and_samtools_tests.yml ├── cwl_draft3_spec │ ├── EDAM.owl │ ├── abc.json │ ├── binding-test.cwl │ ├── bwa-mem-job.json │ ├── bwa-mem-tool.cwl │ ├── cat-job.json │ ├── cat-n-job.json │ ├── cat1-tool.cwl │ ├── cat2-tool.cwl │ ├── cat3-tool.cwl │ ├── cat4-tool.cwl │ ├── cat5-tool.cwl │ ├── conflict-job.json │ ├── conflict-wf.cwl │ ├── count-lines1-wf.cwl │ ├── count-lines2-wf.cwl │ ├── count-lines3-job.json │ ├── count-lines3-wf.cwl │ ├── count-lines4-job.json │ ├── count-lines4-wf.cwl │ ├── count-lines5-wf.cwl │ ├── count-lines6-job.json │ ├── count-lines6-wf.cwl │ ├── count-lines7-wf.cwl │ ├── count-lines8-wf.cwl │ ├── count-lines9-wf.cwl │ ├── dcterms.rdf │ ├── echo-tool.cwl │ ├── empty.json │ ├── env-job.json │ ├── env-tool1.cwl │ ├── env-tool2.cwl │ ├── env-wf1.cwl │ ├── env-wf2.cwl │ ├── foaf.rdf │ ├── formattest-job.json │ ├── formattest.cwl │ ├── formattest2-job.json │ ├── formattest2.cwl │ ├── formattest3.cwl │ ├── glob-expr-list.cwl │ ├── gx_edam.ttl │ ├── hello.tar │ ├── hello.txt │ ├── index.py │ ├── metadata.cwl │ ├── null-expression1-job.json │ ├── null-expression1-tool.cwl │ ├── null-expression2-job.json │ ├── null-expression2-tool.cwl │ ├── number.txt │ ├── optional-output.cwl │ ├── params.cwl │ ├── params2.cwl │ ├── params_inc.yml │ ├── parseInt-job.json │ ├── parseInt-tool.cwl │ ├── record-output-job.json │ ├── record-output.cwl │ ├── ref.fasta │ ├── rename-job.json │ ├── rename.cwl │ ├── revsort-job.json │ ├── revsort.cwl │ ├── revtool.cwl │ ├── scatter-job1.json │ ├── scatter-job2.json │ ├── scatter-valuefrom-job1.json │ ├── scatter-valuefrom-job2.json │ ├── scatter-valuefrom-wf1.cwl │ ├── scatter-valuefrom-wf2.cwl │ ├── scatter-valuefrom-wf3.cwl │ ├── scatter-valuefrom-wf4.cwl │ ├── scatter-wf1.cwl │ ├── scatter-wf2.cwl │ ├── scatter-wf3.cwl │ ├── scatter-wf4.cwl │ ├── schemadef-job.json │ ├── schemadef-tool.cwl │ ├── schemadef-type.yml │ ├── schemadef-wf.cwl │ ├── search-job.json │ ├── search.cwl │ ├── search.py │ ├── shelltest.cwl │ ├── sorttool.cwl │ ├── step-valuefrom-job.json │ ├── step-valuefrom-wf.cwl │ ├── step-valuefrom-wf.json │ ├── step-valuefrom2-wf.cwl │ ├── step-valuefrom3-wf.cwl │ ├── template-tool.cwl │ ├── test-cwl-out.cwl │ ├── tmap-job.json │ ├── tmap-tool.cwl │ ├── underscore.js │ ├── wc-job.json │ ├── wc-tool.cwl │ ├── wc2-tool.cwl │ ├── wc3-tool.cwl │ ├── wc4-tool.cwl │ └── whale.txt ├── demo │ ├── cat.xml │ ├── random_lines_two_pass.py │ ├── randomlines.xml │ └── test-data │ │ ├── 1.bed │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed ├── ga4gh_execution_challenge_phase_1 │ ├── README.md │ ├── job.json │ └── md5sum.input ├── ga4gh_execution_challenge_phase_2 │ └── README.md ├── package_bwa_0_7_7 │ ├── .shed.yml │ └── tool_dependencies.xml ├── package_samtools_0.1.16 │ └── tool_dependencies.xml ├── package_seqtk_1_0_r75 │ ├── .shed.yml │ └── tool_dependencies.xml ├── seqtk_complete │ ├── seqtk_seq.xml │ └── test-data │ │ ├── 2.fasta │ │ └── 2.fastq ├── seqtk_complete_cwl │ ├── seqtk_seq.cwl │ ├── seqtk_seq_job.yml │ ├── seqtk_seq_tests.yml │ └── test-data │ │ ├── 2.fasta │ │ └── 2.fastq └── union_bedgraph │ ├── bedgraph_examples.sh │ ├── output.bedgraph │ ├── unionBedGraphs1.bedgraph │ ├── unionBedGraphs2.bedgraph │ └── unionBedGraphs3.bedgraph ├── pyproject.toml ├── pytest.ini ├── requirements.txt ├── scripts ├── bootstrap_history.py ├── build_slideshow.py ├── categories.py ├── commands_to_rst.py ├── commit_version.py ├── lint_sphinx_output.py ├── new_version.py ├── pre-commit-lint ├── pre-commit-lint-and-test ├── print_version_for_release.py ├── run_doc_test.sh ├── run_galaxy_workflow_tests.sh ├── slideshow_template.html ├── test_conformance_cwl.bash ├── test_wheel.bash ├── test_workflow_tests.sh ├── tool_index.json ├── tool_index_to_id_map.py ├── update_bioconda.bash ├── update_extern.sh ├── update_planemo_recipe.bash └── update_report_assets.sh ├── setup.cfg ├── tests ├── .dockerignore ├── Dockerfile.jenkins ├── __init__.py ├── data │ ├── 1.bed │ ├── Example_Continuous.ibd │ ├── Example_Continuous.imzML │ ├── autopygen │ │ ├── autopygen_actions_cases.py │ │ ├── autopygen_end_to_end_sub.py │ │ ├── autopygen_end_to_end_sub_commands.txt │ │ ├── autopygen_end_to_end_sub_inputs.xml │ │ ├── autopygen_end_to_end_test_case.py │ │ ├── autopygen_generated_commands.txt │ │ ├── autopygen_generated_inputs.xml │ │ └── autopygen_parser_extraction_test_data.py │ ├── cat_list.xml │ ├── cat_pair.xml │ ├── cat_tool.cwl │ ├── cat_tool_job.json │ ├── cat_tool_test.yml │ ├── cat_tool_url.cwl │ ├── cat_tool_url_job.json │ ├── cat_tool_url_test.yml │ ├── collection_creates_pair_2.xml │ ├── composite_input_imzml.xml │ ├── count-lines2-wf.cwl │ ├── data_manager │ │ ├── bowtie2_index_builder.py │ │ ├── data_manager_bowtie2_index_builder │ │ │ ├── data_manager │ │ │ │ ├── bowtie2_index_builder.py │ │ │ │ └── bowtie2_index_builder.xml │ │ │ ├── data_manager_conf.xml │ │ │ ├── test-data │ │ │ │ ├── all_fasta.loc │ │ │ │ ├── bowtie2_data_manager.json │ │ │ │ ├── bowtie2_indices.loc │ │ │ │ ├── phiX174.fasta │ │ │ │ └── tophat2_indices.loc │ │ │ ├── tool-data │ │ │ │ ├── all_fasta.loc.sample │ │ │ │ ├── bowtie2_indices.loc.sample │ │ │ │ └── tophat2_indices.loc.sample │ │ │ ├── tool_data_table_conf.xml.sample │ │ │ └── tool_data_table_conf.xml.test │ │ └── data_manager_fetch_genome_dbkeys_all_fasta │ │ │ ├── data_manager │ │ │ ├── data_manager_fetch_genome_all_fasta_dbkeys.py │ │ │ └── data_manager_fetch_genome_all_fasta_dbkeys.xml │ │ │ ├── data_manager_conf.xml │ │ │ ├── test-data │ │ │ ├── all_fasta.loc │ │ │ ├── dbkeys.loc │ │ │ ├── phiX174.data_manager_json │ │ │ └── phiX174.fasta │ │ │ ├── tool-data │ │ │ ├── all_fasta.loc.sample │ │ │ └── dbkeys.loc.sample │ │ │ ├── tool_data_table_conf.xml.sample │ │ │ └── tool_data_table_conf.xml.test │ ├── hello.txt │ ├── hello_regex.txt │ ├── hello_sed_cut.txt │ ├── hello_truncated.txt │ ├── int_tool.cwl │ ├── int_tool_job.json │ ├── int_tool_test.yml │ ├── issue381.json │ ├── json_value_out-tests.yml │ ├── json_value_out.yml │ ├── lint_skip_list.txt │ ├── not_hello.txt │ ├── not_hello_regex.txt │ ├── output.txt │ ├── output_tests_tool.cwl │ ├── output_tests_tool_job.json │ ├── output_tests_tool_test.yml │ ├── randomlines_job_1.json │ ├── repos │ │ ├── bad_invalid_tool_xml │ │ │ ├── cat.xml │ │ │ ├── related_file │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── bad_invalid_yaml │ │ │ ├── .shed.yml │ │ │ ├── cat.xml │ │ │ ├── related_file │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── bad_missing_include │ │ │ ├── .shed.yml │ │ │ ├── cat.xml │ │ │ ├── related_file │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── bad_missing_repo_deps │ │ │ ├── .shed.yml │ │ │ └── README.rst │ │ ├── bad_missing_tool_deps │ │ │ ├── .shed.yml │ │ │ └── README.rst │ │ ├── bad_package_category │ │ │ ├── .shed.yml │ │ │ ├── README.rst │ │ │ └── tool_dependencies.xml │ │ ├── bad_readme_md │ │ │ ├── .shed.yml │ │ │ ├── README.md │ │ │ ├── cat.xml │ │ │ ├── related_file │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── bad_readme_rst │ │ │ ├── .shed.yml │ │ │ ├── README.rst │ │ │ ├── cat.xml │ │ │ ├── related_file │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── bad_repo_name │ │ │ ├── .shed.yml │ │ │ └── tool_dependencies.xml │ │ ├── bad_tool_no_citations │ │ │ ├── cat.xml │ │ │ ├── related_file │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── conda_exercises_fleeqtk │ │ │ ├── fleeqtk_seq.xml │ │ │ └── test-data │ │ │ │ ├── 2.fasta │ │ │ │ └── 2.fastq │ │ ├── datamash │ │ │ ├── .shed.yml │ │ │ ├── datamash-ops.xml │ │ │ ├── datamash-reverse.xml │ │ │ ├── datamash-transpose.xml │ │ │ ├── macros.xml │ │ │ ├── test-data │ │ │ │ ├── datamash_reverse_input.txt │ │ │ │ ├── datamash_reverse_output.txt │ │ │ │ ├── datamash_transpose_input.txt │ │ │ │ ├── datamash_transpose_output.txt │ │ │ │ ├── group_compute_input.txt │ │ │ │ └── group_compute_output.txt │ │ │ └── tool_dependencies.xml │ │ ├── fastqc │ │ │ ├── .shed.yml │ │ │ ├── fastqc.xml │ │ │ └── tool_dependencies.xml │ │ ├── multi_repos_flat_configured │ │ │ ├── .shed.yml │ │ │ ├── cat1.xml │ │ │ ├── cat2.xml │ │ │ ├── macros.xml │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── multi_repos_flat_configured_complex │ │ │ ├── .shed.yml │ │ │ ├── cat1.xml │ │ │ ├── cat2.xml │ │ │ ├── macros.xml │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── multi_repos_flat_configured_owners │ │ │ ├── .shed.yml │ │ │ ├── cat1.xml │ │ │ ├── cat2.xml │ │ │ ├── macros.xml │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── multi_repos_flat_flag │ │ │ ├── .shed.yml │ │ │ ├── cat1.xml │ │ │ ├── cat2.xml │ │ │ ├── macros.xml │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── multi_repos_flat_flag_suite │ │ │ ├── .shed.yml │ │ │ ├── cat1.xml │ │ │ ├── cat2.xml │ │ │ ├── macros.xml │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── multi_repos_nested.xunit-bad.xml │ │ ├── multi_repos_nested.xunit.xml │ │ ├── multi_repos_nested │ │ │ ├── cat1 │ │ │ │ ├── .shed.yml │ │ │ │ ├── cat1.xml │ │ │ │ ├── macros.xml │ │ │ │ └── test-data │ │ │ │ │ ├── 1.bed │ │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ │ ├── cat2 │ │ │ │ ├── .shed.yml │ │ │ │ ├── cat2.xml │ │ │ │ ├── macros.xml │ │ │ │ └── test-data │ │ │ │ │ ├── 1.bed │ │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ │ └── macros.xml │ │ ├── package_1 │ │ │ ├── .shed.yml │ │ │ ├── README.rst │ │ │ └── tool_dependencies.xml │ │ ├── package_1_changed │ │ │ ├── .shed.yml │ │ │ ├── README.rst │ │ │ └── tool_dependencies.xml │ │ ├── shared_files │ │ │ ├── CITATION │ │ │ └── extra_test_data │ │ │ │ └── extra_test_file.txt │ │ ├── single_tool │ │ │ ├── .shed.yml │ │ │ ├── cat.xml │ │ │ ├── related_file │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── single_tool_exclude │ │ │ ├── .shed.yml │ │ │ ├── cat.xml │ │ │ ├── related_file │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── single_tool_other_owner │ │ │ ├── .shed.yml │ │ │ ├── cat.xml │ │ │ ├── related_file │ │ │ └── test-data │ │ │ │ ├── 1.bed │ │ │ │ └── 1_bed_random_lines_1_seed_asdf_out.bed │ │ ├── suite_1 │ │ │ ├── README.rst │ │ │ └── repository_dependencies.xml │ │ ├── suite_auto │ │ │ └── .shed.yml │ │ ├── up_root │ │ │ ├── .shed.yml │ │ │ ├── README.rst │ │ │ └── cat.xml │ │ └── workflow_1 │ │ │ ├── .shed.yml │ │ │ ├── README.rst │ │ │ ├── blast_top_hit_species.ga │ │ │ └── repository_dependencies.xml │ ├── scheduling_failure_workflows │ │ ├── dataset_failed-test.yml │ │ ├── dataset_failed.yml │ │ ├── invalid_when_expression-test.yml │ │ ├── invalid_when_expression.yml │ │ ├── output_not_found-test.yml │ │ └── output_not_found.yml │ ├── shed-wf2.gxwf-test.yml │ ├── shed-wf2.gxwf.yml │ ├── test_workflow_1.ga │ ├── tools │ │ ├── bwa_invalid_version.xml │ │ ├── bwa_without_requirements.xml │ │ ├── bwa_wrong_version.xml │ │ ├── empty_cdata.xml │ │ ├── empty_cdata_macros.xml │ │ ├── fail_bad_profile_1.xml │ │ ├── fail_bad_profile_2.xml │ │ ├── fail_bad_profile_3.xml │ │ ├── fail_citation.xml │ │ ├── fail_cond_param_extra_boolean_when.xml │ │ ├── fail_cond_param_extra_when.xml │ │ ├── fail_cond_param_missing_boolean_when.xml │ │ ├── fail_cond_param_missing_when.xml │ │ ├── fail_conditional_test_optional.xml │ │ ├── fail_data_name.xml │ │ ├── fail_format.xml │ │ ├── fail_id_space.yml │ │ ├── fail_name_mismatch.xml │ │ ├── fail_order.xml │ │ ├── fail_output_collection_name_mismatch.xml │ │ ├── fail_output_collection_name_missing.xml │ │ ├── fail_select_param_opts.xml │ │ ├── fail_test_no_expects.xml │ │ ├── fail_xml_invalid.xml │ │ ├── functional_test_tools │ │ │ └── job_properties.xml │ │ ├── invalid_doi.xml │ │ ├── ok-cat1-tool.cwl │ │ ├── ok_conditional.xml │ │ ├── ok_param_argument.xml │ │ ├── ok_select_param.xml │ │ ├── ok_test_assert_command.xml │ │ ├── ok_test_expects.xml │ │ ├── ok_test_output_collections.xml │ │ ├── timeout.xml │ │ └── url.xml │ ├── training_metadata.yaml │ ├── training_query_tabular.json │ ├── training_tutorial.md │ ├── training_tutorial_wo_zenodo.md │ ├── training_wf_param_values.json │ ├── training_workflow.ga │ ├── tt_fail.html │ ├── tt_fail.json │ ├── tt_fail.xml │ ├── tt_success.html │ ├── tt_success.json │ ├── tt_success.xml │ ├── tutorial.md │ ├── wf1.ga │ ├── wf1.gxwf-job-url.yml │ ├── wf1.gxwf-job.yml │ ├── wf1.gxwf-test.yml │ ├── wf1.gxwf.yml │ ├── wf10-tags-and-rules.gxwf-test.yml │ ├── wf10-tags-and-rules.gxwf.yml │ ├── wf11-remote.gxwf-test.yml │ ├── wf13_tool_shed_repository_gxformat2-test.yml │ ├── wf13_tool_shed_repository_gxformat2.yml │ ├── wf14-unlinted-best-practices.ga │ ├── wf14-unlinted-best-practices.yml │ ├── wf15-test-assertions-test.yml │ ├── wf15-test-assertions.yml │ ├── wf16_optional_input_output_label-test.yml │ ├── wf16_optional_input_output_label.ga │ ├── wf17_sanitize_output_paths-test.yml │ ├── wf17_sanitize_output_paths.yml │ ├── wf18_simple_conditional-test.yml │ ├── wf18_simple_conditional.yml │ ├── wf19-unlinted-author-identifier-best-practices.ga │ ├── wf2-job.yml │ ├── wf2-test.yml │ ├── wf2.ga │ ├── wf4-distro-tools.gxwf-test.yml │ ├── wf4-distro-tools.gxwf.yml │ ├── wf5-collection-input.gxwf-test.yml │ ├── wf5-collection-input.gxwf.yml │ ├── wf6-composite-inputs.gxwf-test.yml │ ├── wf6-composite-inputs.gxwf.yml │ ├── wf7-collection-output-fail.gxwf-test.yml │ ├── wf7-collection-output-fail.gxwf.yml │ ├── wf7-collection-output.gxwf-test.yml │ ├── wf7-collection-output.gxwf.yml │ ├── wf8-collection-nested-input.gxwf-test.yml │ ├── wf8-collection-nested-input.gxwf.yml │ ├── wf9-int-input.gxwf-test.yml │ ├── wf9-int-input.gxwf.yml │ ├── wf_failed_step-test.yml │ ├── wf_failed_step.ga │ ├── wf_repos │ │ ├── autoupdate_tests │ │ │ ├── diff-refactor-test.ga │ │ │ ├── diff-refactor-test.gxwf.yml │ │ │ ├── wf_autoupdate_test_multiple_repos.ga │ │ │ ├── workflow_with_unexisting_tool.ga │ │ │ └── workflow_with_unexisting_version_of_tool.ga │ │ ├── basic_format2_collection_wrong_assert │ │ │ ├── basic_format2.gxwf-test.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_collection_wrong_assert_list │ │ │ ├── basic_format2.gxwf-test.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_dockstore │ │ │ ├── .dockstore.yml │ │ │ ├── basic_format2.gxwf-tests.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_dockstore_empty │ │ │ ├── .dockstore.yml │ │ │ ├── basic_format2.gxwf-tests.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_dockstore_invalid_yaml │ │ │ ├── .dockstore.yml │ │ │ ├── basic_format2.gxwf-tests.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_dockstore_misspelled_primary_key │ │ │ ├── .dockstore.yml │ │ │ ├── basic_format2.gxwf-tests.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_dockstore_wrong_descriptor │ │ │ ├── .dockstore.yml │ │ │ ├── basic_format2.gxwf-tests.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_dockstore_wrong_test_file │ │ │ ├── .dockstore.yml │ │ │ ├── basic_format2.gxwf-tests.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_input_missing │ │ │ ├── basic_format2.gxwf-test.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_input_misspelled │ │ │ ├── basic_format2.gxwf-tests.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_missing_input │ │ │ ├── basic_format2.gxwf-test.yml │ │ │ └── basic_format2.gxwf.yml │ │ ├── basic_format2_ok │ │ │ ├── basic_format2.gxwf-test.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_ok_collection │ │ │ ├── basic_format2.gxwf-test.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_ok_list │ │ │ ├── basic_format2.gxwf-test.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_output_misnamed │ │ │ ├── basic_format2.gxwf-test.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_format2_wrong_assert_list │ │ │ ├── basic_format2.gxwf-test.yml │ │ │ ├── basic_format2.gxwf.yml │ │ │ └── hello.txt │ │ ├── basic_native_ok │ │ │ ├── basic_native-test.yml │ │ │ ├── basic_native.yml │ │ │ └── hello.txt │ │ ├── basic_wf_iwc_invalid_version │ │ │ ├── .dockstore.yml │ │ │ ├── CHANGELOG.md │ │ │ ├── README.md │ │ │ ├── Super-simple-workflow-tests.yml │ │ │ └── Super-simple-workflow.ga │ │ ├── copy_lint_examples.sh │ │ └── from_format2 │ │ │ ├── 0_basic_format2 │ │ │ └── 0_basic_format2.yml │ │ │ ├── 0_basic_native │ │ │ └── 0_basic_native.yml │ │ │ ├── 1_format2_step_errors │ │ │ └── 1_format2_step_errors.yml │ │ │ └── 1_native_no_output_labels │ │ │ └── 1_native_no_output_labels.yml │ ├── wf_same_name_outputs-tests.yml │ ├── wf_same_name_outputs.ga │ ├── wf_same_name_outputs_input.txt │ ├── xunit_failure.xml │ ├── xunit_nose_0_11.xml │ └── xunit_nose_1_3.xml ├── repository_dependencies.xml ├── repository_dependencies_shed.xml ├── scripts │ └── conda_test.sh ├── shed_app.py ├── shed_app_test_utils.py ├── test_add_argument_actions_autopygen.py ├── test_allure.py ├── test_autopygen_parser_discovery.py ├── test_autoupdate.py ├── test_build_and_lint.py ├── test_cmd_autoupdate.py ├── test_cmd_dockstore_init.py ├── test_cmd_download_invocation_export.py ├── test_cmd_invocation_export.py ├── test_cmd_job_config_init.py ├── test_cmd_merge_reports.py ├── test_cmd_profile_job_config_init.py ├── test_cmd_serve.py ├── test_cmd_shed_test.py ├── test_cmd_test.py ├── test_cmd_test_conda.py ├── test_cmd_test_reports.py ├── test_cmd_training_fill_data_library.py ├── test_cmd_training_generate_from_wf.py ├── test_cmd_training_init.py ├── test_cmd_workflow_convert.py ├── test_cmd_workflow_job_init.py ├── test_cmd_workflow_lint.py ├── test_cmd_workflow_test_init.py ├── test_cmds_with_workflow_id.py ├── test_collection_elements_to_test_def.py ├── test_command_io.py ├── test_config_init.py ├── test_database_commands.py ├── test_engines.py ├── test_external_galaxy_commands.py ├── test_galaxy_config.py ├── test_galaxy_serve.py ├── test_galaxy_workflow_utils.py ├── test_git.py ├── test_github_create_release.py ├── test_init_and_test.py ├── test_invocation_polling.py ├── test_io.py ├── test_lint.py ├── test_normalize.py ├── test_planemo.py ├── test_profile_commands.py ├── test_run.py ├── test_shed.py ├── test_shed_create.py ├── test_shed_diff.py ├── test_shed_diff_xml.py ├── test_shed_download.py ├── test_shed_expansion.py ├── test_shed_init.py ├── test_shed_lint.py ├── test_shed_operations.py ├── test_shed_test.py ├── test_shed_upload.py ├── test_test_checker.py ├── test_test_engines.py ├── test_training.py ├── test_training_tool_input.py ├── test_training_topic.py ├── test_training_tutorial.py ├── test_training_utils.py ├── test_utils.py ├── test_validation.py ├── test_workflow_lint.py ├── test_workflow_progress.py ├── test_workflow_simulation.py ├── test_xml_diff.py ├── tool_dependencies_good_1.xml ├── tool_dependencies_good_2.xml ├── xml_bad_1.xml ├── xml_good_1.xml ├── xml_good_2.xml ├── xsd_command.xsd └── xsd_schema_1.xsd └── tox.ini /.coveragerc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/planemo/HEAD/.coveragerc -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/galaxyproject/planemo/HEAD/.editorconfig 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