mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
46e83e178d
These are available in a list(n) x list (m) -> list(nxm) version (a cross product that produces two flat lists) and a list(n) x list(m) -> list(n):list(m) version (a cross product that produces two nested lists). After two lists have been run through one of these two tools - the result is two new lists that can be passed into another tool to perform all-against-all operations using Galaxy's normal collection mapping semantics. The choice of which to use will depend on how you want to continue to process the all-against-all results after the next step in an analysis. My sense is the flat version is "easier" to think about and pick through manually and the nested version perserves more structure if additional collection operation tools will be used to filter or aggregate the results. Some considerations: Apply Rules? I do not believe the Apply Rules tool semanatics would allow these operations but certainly the Apply Rules tool could be used to convert the result of the flat version to the nested version or vice versa - so no metadata is really lost per se between the two versions. I think it is still worth including both versions though - they both have utility (both for instance are baked into CWL's workflow semantics - https://docs.sevenbridges.com/docs/about-parallelizing-tool-executions#nested-cross-product) and avoiding requiring complex Apply Rules programs for simple workflows is probably ideal. One Tool vs Two? Marius and I agree that few simpler tools for these kinds of operations are better. The tool help can be more focused and avoiding the conditional and conditional outputs make the static analysis done for instance by the workflow editor simpler.
315 lines
14 KiB
XML
315 lines
14 KiB
XML
<?xml version="1.0"?>
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<toolbox tool_path="${tool_conf_dir}" is_shed_conf="false">
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<tool file="upload.xml" />
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<tool file="export_remote.xml" />
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<section id="test" name="Test Section">
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<tool file="multi_data_optional.xml" />
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<tool file="paths_as_file.xml" />
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<tool file="param_text_option.xml" />
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<tool file="column_param.xml" />
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</section>
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<tool file="image_diff.xml"/>
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<tool file="output_format_input.xml"/>
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<tool file="ucsc_tablebrowser.xml"/>
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<tool file="test_data_source.xml"/>
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<tool file="simple_constructs.xml" />
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<tool file="color_param.xml" />
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<tool file="inheritance_simple.xml" />
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<tool file="boolean_conditional.xml" />
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<tool file="composite.xml" />
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<tool file="environment_variables.xml" />
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<tool file="environment_variables_inject.xml" />
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<tool file="code_file.xml" />
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<tool file="disambiguate_cond.xml" />
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<tool file="multi_repeats.xml" />
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<tool file="remove_value.xml" />
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<tool file="bibtex.xml" />
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<tool file="select_from_url.xml" />
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<tool file="multi_select.xml" />
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<tool file="multi_output.xml" />
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<tool file="multi_output_configured.xml" />
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<tool file="multi_output_assign_primary.xml" />
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<tool file="multi_output_assign_primary_ext_dbkey.xml" />
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<tool file="multi_output_recurse.xml" />
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<tool file="multi_output_recurse_collection.xml" />
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<tool file="galaxy_json_discover_and_sleep.xml" />
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<tool file="tool_provided_metadata_1.xml" />
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<tool file="tool_provided_metadata_2.xml" />
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<tool file="tool_provided_metadata_3.xml" />
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<tool file="tool_provided_metadata_4.xml" />
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<tool file="tool_provided_metadata_5.xml" />
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<tool file="tool_provided_metadata_6.xml" />
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<tool file="tool_provided_metadata_7.xml" />
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<tool file="tool_provided_metadata_8.xml" />
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<tool file="tool_provided_metadata_9.xml" />
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<tool file="tool_provided_metadata_10.xml" />
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<tool file="tool_provided_metadata_11.xml" />
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<tool file="tool_provided_metadata_12.xml" />
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<tool file="empty_datasets.xml" />
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<tool file="is_of_type.xml" />
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<tool file="data_optional.xml" />
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<tool file="inputs_as_json.xml" />
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<tool file="inputs_as_json_profile.xml" />
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<tool file="inputs_as_json_with_paths.xml" />
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<tool file="inputs_as_json_with_staging_path_and_source_path.xml" />
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<tool file="filter_multiple_splitter.xml" />
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<tool file="filter_param_value.xml" />
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<tool file="filter_param_value_ref_attribute.xml" />
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<tool file="filter_static_regexp.xml" />
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<tool file="select_from_dataset.xml" />
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<tool file="select_from_dataset_in_conditional.xml" />
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<tool file="select_from_csvdataset.xml" />
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<tool file="select_from_dataset_optional.xml" />
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<tool file="drill_down.xml" />
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<tool file="dbkey_filter_input.xml" />
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<tool file="dbkey_filter_multi_input.xml" />
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<tool file="dbkey_filter_collection.xml" />
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<tool file="dbkey_output_action.xml" />
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<tool file="composite_output.xml" />
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<tool file="composite_output_tests.xml" />
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<tool file="unicode_stream.xml" />
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<tool file="vcf_bgzip.xml" />
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<tool file="metadata.xml" />
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<tool file="metadata_bam.xml" />
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<tool file="discover_metadata_files.xml" />
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<tool file="metadata_bcf.xml" />
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<tool file="metadata_bed.xml" />
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<tool file="metadata_biom1.xml" />
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<tool file="metadata_check_eq.xml" />
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<tool file="metadata_column_names.xml" />
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<tool file="strict_shell.xml" />
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<tool file="strict_shell_default_off.xml" />
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<tool file="strict_shell_profile.xml" />
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<tool file="detect_errors.xml" />
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<tool file="detect_errors_aggressive.xml" />
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<tool file="qc_stdout.xml" />
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<tool file="directory_uri.xml" />
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<tool file="md5sum.xml" />
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<tool file="checksum.xml" />
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<tool file="sim_size_delta.xml" />
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<tool file="composite_shapefile.xml" />
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<tool file="is_valid_xml.xml" />
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<tool file="expression_tools/parse_values_from_file.xml"/>
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<tool file="expression_tools/pick_value.xml" />
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<!--
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TODO: Figure out why this transiently fails on Jenkins.
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<tool file="maxseconds.xml" />
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-->
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<tool file="job_properties.xml" />
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<tool file="job_environment_default.xml" />
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<tool file="job_environment_default_legacy.xml" />
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<tool file="job_environment_explicit_shared_home.xml" />
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<tool file="job_environment_explicit_isolated_home.xml" />
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<tool file="galaxy_slots_and_memory.xml" />
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<tool file="version_command_plain.xml" />
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<tool file="version_command_interpreter.xml" />
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<tool file="version_command_tool_dir.xml" />
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<tool file="exit_code_oom.xml" />
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<tool file="exit_code_from_file.xml" />
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<tool file="exit_code_from_env.xml" />
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<tool file="gzipped_inputs.xml" />
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<tool file="options_from_metadata_file.xml" />
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<tool file="output_order.xml" />
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<tool file="output_format.xml" />
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<tool file="output_format_deprecated_when.xml" />
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<tool file="output_format_collection.xml" />
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<tool file="format_source_in_conditional.xml" />
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<tool file="output_filter.xml" />
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<tool file="output_empty_work_dir.xml" />
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<tool file="output_filter_with_input.xml" />
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<tool file="output_filter_with_input_optional.xml" />
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<tool file="output_filter_exception_1.xml" />
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<tool file="output_collection_filter.xml" />
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<tool file="output_auto_format.xml" />
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<tool file="create_2.xml" />
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<tool file="create_10.xml" />
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<tool file="disambiguate_repeats.xml" />
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<tool file="min_repeat.xml" />
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<tool file="parallelism.xml" />
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<tool file="parallelism_optional.xml" />
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<tool file="implicit_default_conds.xml" />
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<tool file="multi_data_param.xml" />
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<tool file="multi_data_repeat.xml" />
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<tool file="multi_data_optional.xml" />
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<tool file="paths_as_file.xml" />
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<tool file="param_text_option.xml" />
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<tool file="column_param.xml" />
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<tool file="column_param_configfile.xml" />
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<tool file="column_param_list.xml" />
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<tool file="column_multi_param.xml" />
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<tool file="select_optional.xml"/>
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<tool file="select_dynamic.xml"/>
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<tool file="hidden_param.xml" />
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<tool file="special_params.xml" />
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<tool file="section.xml" />
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<tool file="sam_to_unsorted_bam.xml" />
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<tool file="top_level_data.xml" />
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<tool file="validation_hdf5.xml" />
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<tool file="validation_image.xml"/>
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<tool file="validation_zip.xml" />
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<tool file="validation_tar.xml" />
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<tool file="validation_tar_gz.xml" />
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<tool file="validation_default.xml" />
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<tool file="validation_sanitizer.xml" />
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<tool file="validation_repeat.xml" />
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<tool file="validation_metadata_in_range.xml"/>
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<tool file="validation_metadata_in_datatable.xml"/>
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<tool file="validation_dataset_metadata_in_file.xml"/>
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<tool file="validation_value_in_datatable.xml"/>
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<tool file="empty_output.xml" />
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<tool file="validation_empty_dataset.xml" />
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<tool file="implicit_conversion.xml" />
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<tool file="implicit_conversion_format_input.xml" />
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<tool file="implicit_conversion_optional_param.xml" />
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<tool file="implicit_collection_conversion.xml" />
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<tool file="implicit_nested_list_conversion.xml" />
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<tool file="explicit_conversion.xml" />
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<tool file="identifier_source.xml" />
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<tool file="identifier_single.xml" />
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<tool file="identifier_single_in_repeat.xml" />
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<tool file="identifier_in_conditional.xml" />
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<tool file="identifier_multiple.xml" />
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<tool file="identifier_multiple_in_conditional.xml" />
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<tool file="identifier_multiple_in_repeat.xml" />
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<tool file="identifier_collection.xml" />
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<tool file="identifier_all_collection_types.xml"/>
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<tool file="identifier_in_actions.xml" />
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<tool file="fail_identifier.xml" />
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<tool file="fail_writing_work_dir_file.xml" />
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<tool file="tool_directory.xml" />
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<tool file="tool_directory_docker.xml" />
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<tool file="output_action_change_format.xml" />
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<tool file="output_action_change_format_paired.xml" />
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<tool file="collection_paired_test.xml" />
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<tool file="collection_paired_default.xml" />
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<tool file="collection_paired_structured_like.xml" />
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<tool file="collection_paired_conditional_structured_like.xml" />
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<tool file="collection_nested_test.xml" />
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<tool file="collection_nested_default.xml" />
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<tool file="collection_mixed_param.xml" />
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<tool file="collection_two_paired.xml" />
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<tool file="collection_creates_pair.xml" />
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<tool file="collection_creates_pair_format.xml" />
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<tool file="collection_creates_pair_from_type.xml" />
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<tool file="collection_creates_pair_from_work_dir.xml" />
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<tool file="collection_creates_list.xml" />
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<tool file="collection_creates_list_2.xml" />
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<tool file="collection_creates_list_of_pairs.xml" />
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<tool file="collection_optional_param.xml" />
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<tool file="collection_split_on_column.xml" />
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<tool file="collection_creates_dynamic_nested.xml" />
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<tool file="collection_creates_dynamic_nested_from_json.xml" />
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<tool file="collection_creates_dynamic_nested_from_json_elements.xml" />
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<tool file="collection_creates_dynamic_list_of_pairs.xml" />
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<tool file="collection_type_source.xml" />
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<tool file="collection_type_source_map_over.xml" />
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<tool file="collection_creates_list_fail.xml" />
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<tool file="collection_creates_dynamic_nested_fail.xml" />
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<tool file="collection_cat_group_tag.xml" />
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<tool file="collection_cat_group_tag_multiple.xml" />
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<tool file="discover_sort_by.xml" />
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<tool file="expression_forty_two.xml" />
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<tool file="expression_pick_larger_file.xml" />
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<tool file="expression_parse_int.xml" />
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<tool file="expression_log_line_count.xml" />
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<tool file="expression_null_handling_boolean.xml" />
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<tool file="expression_null_handling_integer.xml" />
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<tool file="expression_null_handling_float.xml" />
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<tool file="expression_null_handling_text.xml" />
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<tool file="cheetah_casting.xml" />
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<tool file="cheetah_problem_unbound_var.xml" />
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<tool file="cheetah_problem_unbound_var_input.xml" />
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<tool file="cheetah_problem_syntax_error.xml" />
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<tool file="model_attributes.xml" />
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<tool file="python_environment_problem.xml" />
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<tool file="config_vars.xml" />
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<tool file="expect_num_outputs.xml" />
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<tool file="text_repeat.xml" />
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<tool file="integer_default.xml" />
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<tool file="multiple_versions_v01.xml" />
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<tool file="multiple_versions_v01galaxy6.xml" />
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<tool file="multiple_versions_v02.xml" />
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<section id="test_section_multi" name="Test Section with Multiple Versions">
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<tool file="multiple_versions_v01.xml" />
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<tool file="multiple_versions_v01galaxy6.xml" />
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<tool file="multiple_versions_v02.xml" />
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</section>
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<tool file="multiple_versions_changes_v01.xml" />
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<tool file="multiple_versions_changes_v02.xml" />
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<tool file="interactivetool_simple.xml" />
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<tool file="interactivetool_two_entry_points.xml" />
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<tool file="converter_target_datatype.xml" />
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<!-- Tools interesting only for building up test workflows. -->
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<!-- Next three tools demonstrate concatenating multiple datasets
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with a repeat, multiple datasets with a multiple input data
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parameter, and multiple datasets from a collection. -->
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<tool file="for_workflows/cat.xml" />
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<tool file="for_workflows/cat_list.xml" />
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<tool file="for_workflows/cat_default.xml" />
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<tool file="for_workflows/cat_collection.xml" />
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<tool file="for_workflows/head.xml" />
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<tool file="for_workflows/cat_interleave.xml" />
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<tool file="for_workflows/pileup.xml" />
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<tool file="for_workflows/mapper.xml" />
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<tool file="for_workflows/mapper2.xml" />
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<tool file="for_workflows/mapper_two.xml" />
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<tool file="for_workflows/split.xml" />
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<tool file="for_workflows/empty_list.xml" />
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<tool file="for_workflows/count_list.xml" />
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<tool file="for_workflows/count_multi_file.xml" />
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<tool file="for_workflows/create_input_collection.xml" />
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<tool file="for_workflows/randomlines.xml" />
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<section id="filter" name="For Tours">
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<tool file="for_tours/filtering.xml" />
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</section>
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<!-- Tools for dependency and container testing. -->
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<tool file="legacy_r.xml" />
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<tool file="mulled_example_multi_1.xml" />
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<tool file="mulled_example_multi_versionless.xml" />
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<tool file="mulled_example_multi_incomplete.xml" />
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<tool file="mulled_example_conflict.xml" />
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<tool file="mulled_example_simple.xml" />
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<tool file="mulled_example_explicit.xml" />
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<tool file="mulled_example_invalid_case.xml" />
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<tool file="mulled_example_broken_no_requirements.xml" />
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<tool file="mulled_example_broken_no_requirements_fallback.xml" />
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<tool file="explicit_container.xml" />
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<tool file="explicit_singularity_container.xml"/>
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<tool file="simple_constructs.yml" />
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<tool file="from_work_dir_glob.xml" />
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<!-- Tools without tool test but useful for hand-crafted, artisanal test cases. -->
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<tool file="cat_data_and_sleep.xml" />
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<!-- Load collection operation tools - I consider these part of the
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"framework" and they are used to in API tests to test the underlying
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ToolActions. -->
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<tool file="${model_tools_path}/unzip_collection.xml" />
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<tool file="${model_tools_path}/zip_collection.xml" />
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<tool file="${model_tools_path}/filter_failed_collection.xml" />
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<tool file="${model_tools_path}/keep_success_collection.xml" />
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<tool file="${model_tools_path}/filter_empty_collection.xml" />
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<tool file="${model_tools_path}/flatten_collection.xml" />
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<tool file="${model_tools_path}/sort_collection_list.xml" />
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<tool file="${model_tools_path}/harmonize_two_collections_list.xml" />
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<tool file="${model_tools_path}/merge_collection.xml" />
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<tool file="${model_tools_path}/relabel_from_file.xml" />
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<tool file="${model_tools_path}/filter_from_file.xml" />
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<tool file="${model_tools_path}/cross_product_flat.xml" />
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<tool file="${model_tools_path}/cross_product_nested.xml" />
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<tool file="${model_tools_path}/tag_collection_from_file.xml" />
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<tool file="${model_tools_path}/apply_rules.xml" />
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<tool file="${model_tools_path}/build_list.xml" />
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<tool file="${model_tools_path}/build_list_1.2.0.xml" />
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<tool file="${model_tools_path}/extract_dataset.xml" />
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<tool file="${model_tools_path}/duplicate_file_to_collection.xml" />
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</toolbox>
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