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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
72e361bcf1
without needing to specify a discovered dataset pattern. If the ``discovered_datasets`` tag includes ``from_tool_provided_metadata="true"`` the datsets listed in galaxy.json will just be used directly without needing to be "discovered" using a dataset pattern. Metadata and such can continue to be specified either in that file or on the discovered_dataset element except things like pattern (which is not used) and sort_by (since the json should describe the order I suppose).
79 lines
2.8 KiB
XML
79 lines
2.8 KiB
XML
<tool id="collection_creates_dynamic_nested_from_json" name="collection_creates_dynamic_nested_from_json" version="0.1.0" profile="17.09">
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<command>
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echo "A" > oe1_ie1.fq ;
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echo "B" > oe1_ie2.fq ;
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echo "C" > oe2_ie1.fq ;
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echo "D" > oe2_ie2.fq ;
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echo "E" > oe3_ie1.fq ;
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echo "F" > oe3_ie2.fq ;
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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">{"list_output": {
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"datasets": [
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{"identifier_0": "oe1", "identifier_1": "ie1", "filename": "oe1_ie1.fq"},
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{"identifier_0": "oe1", "identifier_1": "ie2", "filename": "oe1_ie2.fq"},
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{"identifier_0": "oe2", "identifier_1": "ie1", "filename": "oe2_ie1.fq"},
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{"identifier_0": "oe2", "identifier_1": "ie2", "filename": "oe2_ie2.fq"},
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{"identifier_0": "oe3", "identifier_1": "ie1", "filename": "oe3_ie1.fq"},
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{"identifier_0": "oe3", "identifier_1": "ie2", "filename": "oe3_ie2.fq"}
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]}}</configfile>
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</configfiles>
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<inputs>
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<param name="foo" type="text" label="Dummy Parameter" />
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</inputs>
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<outputs>
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<collection name="list_output" type="list:list" label="Duplicate List">
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<!-- Use named regex group to grab pattern
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<identifier_0>_<identifier_1>.fq. Here identifier_0 is the list
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identifier of the outer list and identifier_1 is the list identifier
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of the inner list (for instance oe1_ie2.fq in above example).
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-->
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<discover_datasets from_provided_metadata="true" ext="fastqsanger" visible="true" />
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</collection>
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</outputs>
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<tests>
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<test>
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<param name="foo" value="bar" />
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<output_collection name="list_output" type="list:list">
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<element name="oe1">
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<element name="ie1">
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<assert_contents>
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<has_text_matching expression="^A\n$" />
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</assert_contents>
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</element>
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<element name="ie2">
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<assert_contents>
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<has_text_matching expression="^B\n$" />
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</assert_contents>
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</element>
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</element>
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<element name="oe2">
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<element name="ie1">
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<assert_contents>
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<has_text_matching expression="^C\n$" />
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</assert_contents>
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</element>
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<element name="ie2">
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<assert_contents>
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<has_text_matching expression="^D\n$" />
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</assert_contents>
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</element>
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</element>
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<element name="oe3">
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<element name="ie1">
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<assert_contents>
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<has_text_matching expression="^E\n$" />
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</assert_contents>
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</element>
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<element name="ie2">
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<assert_contents>
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<has_text_matching expression="^F\n$" />
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</assert_contents>
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</element>
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</element>
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</output_collection>
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</test>
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</tests>
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</tool>
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