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71 lines
2.4 KiB
XML
71 lines
2.4 KiB
XML
<tool id="collection_creates_dynamic_nested" name="collection_creates_dynamic_nested" version="0.1.0" profile="16.04">
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<command><![CDATA[
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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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sleep '$sleep_time';
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exit $fail_bool
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]]></command>
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<inputs>
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<param name="foo" type="text" label="Dummy Parameter" />
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<param name="sleep_time" type="integer" label="Sleep Time" value="0" />
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<param name="fail_bool" type="boolean" label="Fail tool run?" truevalue="1" falsevalue="0"/>
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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 pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.fq" 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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