mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-11-02 03:33:04 +08:00
John Chilton
9e471d3e97
If one maps a tool over an empty collection, one should get an empty output collection for each of the tool's outputs. This should have always been a valid operation I think, the code just wasn't quite structured right when the collection work was merged - there were too many places I was assuming the existence of at least one actual output or input that was mapped over to continue going. This reworks all of that and seems to handle empty collections appropriately. Fixes #4025 (not being informing the user of the operation, but actually by allowing the operation - which it should be allowed I think).
177 lines
7.2 KiB
XML
177 lines
7.2 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="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="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="library_data.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="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="empty_datasets.xml" />
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<tool file="inputs_as_json.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_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="metadata_bcf.xml" />
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<tool file="metadata_biom1.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="detect_errors_aggressive.xml" />
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<tool file="md5sum.xml" />
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<tool file="checksum.xml" />
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<tool file="is_valid_xml.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="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_from_file.xml" />
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<tool file="gzipped_inputs.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="output_filter.xml" />
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<tool file="output_filter_with_input.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_multi_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="top_level_data.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="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="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_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="tool_directory.xml" />
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<tool file="output_action_change_format.xml" />
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<tool file="collection_paired_test.xml" />
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<tool file="paired_collection_map_over_structured_like.xml" />
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<tool file="collection_nested_test.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_from_type.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_creates_list_fail.xml" />
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<tool file="collection_creates_dynamic_nested_fail.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="python_environment_problem.xml" />
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<tool file="config_vars.xml" />
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<tool file="multiple_versions_v01.xml" />
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<tool file="multiple_versions_v02.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_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/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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<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="simple_constructs.yml" />
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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="${model_tools_path}/flatten_collection.xml" />
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<tool file="${model_tools_path}/sort_collection_list.xml" />
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<tool file="${model_tools_path}/merge_collection.xml" />
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<tool file="${model_tools_path}/relabel_from_file.xml" />
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<tool file="${model_tools_path}/filter_from_file.xml" />
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</toolbox>
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