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https://github.com/galaxyproject/galaxy.git
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John Chilton
517f248ac4
- Add another test to demonstrate referencing entries in galaxy.json for datasets by dataset path basename instead of ID. - Add a bit more documentation to test tools. - Redo the structure of galaxy.json for profile >= 17.09 tools with two new test tools to demonstrate the new structure - for both output dataset metadata and discovered dataset metadata. - Improved abstractions for interaction between tools and jobs to enable different tool provided metadata collection depending on tool profile version.
45 lines
1.9 KiB
XML
45 lines
1.9 KiB
XML
<tool id="tool_provided_metadata_3" name="tool_provided_metadata_3">
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<!-- Demonstrate setting datatype defined metadata for discovered datasets via galaxy.json for legacy tools (galaxy.json structure changes for profile >= 17.09 tools). -->
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<command>
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echo "1" > sample1.report.tsv;
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echo "2" > sample2.report.tsv;
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cp $c1 galaxy.json;
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</command>
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<configfiles>
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<configfile name="c1">{"type": "new_primary_dataset", "filename": "sample1.report.tsv", "name": "cool name 1", "ext": "txt", "info": "cool 1 info", "dbkey": "hg19", "metadata": {"data_lines": 10, "foo": "bar"}}
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{"type": "new_primary_dataset", "filename": "sample2.report.tsv", "name": "cool name 2", "ext": "txt", "info": "cool 2 info", "dbkey": "hg19", "metadata": {"data_lines": 20, "foo": "bar"}}
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</configfile>
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</configfiles>
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<inputs>
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<param name="input" type="data" />
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</inputs>
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<outputs>
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<data name="sample">
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<discover_datasets pattern="(?P<designation>.+)\.report\.tsv" visible="true" />
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</data>
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</outputs>
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<tests>
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<test>
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<param name="input" ftype="txt" value="simple_line.txt"/>
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<output name="sample">
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<discovered_dataset designation="sample1" ftype="txt">
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<assert_contents><has_line line="1" /></assert_contents>
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<!-- Datatype defined metadata can be overridden/specified directly.
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-->
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<metadata name="data_lines" value="10" />
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<!-- Non-datatype defined metadata values are ignored by the framework.
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Uncommenting the following test will break this test.
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-->
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<!--
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<metadata name="foo" value="bar" />
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-->
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</discovered_dataset>
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<discovered_dataset designation="sample2" ftype="txt">
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<assert_contents><has_line line="2" /></assert_contents>
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<metadata name="data_lines" value="20" />
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</discovered_dataset>
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</output>
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</test>
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</tests>
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</tool>
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