mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-13 00:44:55 +08:00
John Chilton
4de71a0c82
The metadata system will then "sniff" the outputs and set the type appropriately.
Tool used to demonstrate and test this functionality is included, run the test with:
./run_tests.sh -framework -id output_auto_format
If auto_format="true" than explicitly setting ``format="another_type"`` will prevent the tool from loading so that we can allow this to specify a default type later without breaking backward compatiblity.
Update 1:
- Switched from ``format="auto"`` to ``auto_format="true"`` based on Dan's comments (https://github.com/galaxyproject/galaxy/pull/130).
Update 2:
- Updated this to work when setting metadata internally.
- Switch underlying representation of type from ``_auto_`` to ``_sniff_`` based on seeing a new block in ``galaxy.jobs``. ``auto`` indicates the tool should specify the datatype at runtime. This is in some ways the inverse of that (the tool telling Galaxy to detect the type instead of Galaxy telling the tool to) so I decided it would be best to not have ``auto`` and ``_auto_`` doing completely different things.
75 lines
2.7 KiB
XML
75 lines
2.7 KiB
XML
<?xml version="1.0"?>
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<toolbox tool_path="${tool_conf_dir}">
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<tool file="upload.xml"/>
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<tool file="simple_constructs.xml" />
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<tool file="inheritance_simple.xml" />
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<tool file="composite.xml" />
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<tool file="compare_bam_as_sam.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="multi_page.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="composite_output.xml" />
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<tool file="metadata.xml" />
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<tool file="metadata_bam.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="job_properties.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_filter.xml" />
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<tool file="output_auto_format.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="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="identifier_single.xml" />
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<tool file="identifier_multiple.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="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_optional_param.xml" />
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<tool file="collection_split_on_column.xml" />
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<tool file="cheetah_casting.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="simple_constructs.yml" />
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</toolbox>
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