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29 lines
1.1 KiB
XML
29 lines
1.1 KiB
XML
<tool id="metadata_bam" name="metadata BAM" version="1.0.0" profile="16.04">
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<command><![CDATA[
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#assert $input_bam.metadata.bam_index
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echo '${ref_names}' > '${output_of_input_metadata}'
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]]></command>
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<inputs>
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<param name="input_bam" type="data" format="bam" label="BAM File"/>
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<param name="ref_names" type="select" optional="False" label="Select references you would like to restrict bam to" multiple="True">
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<options>
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<filter type="data_meta" ref="input_bam" key="reference_names" />
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</options>
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</param>
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</inputs>
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<outputs>
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<data format="txt" name="output_of_input_metadata" />
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</outputs>
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<tests>
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<test>
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<param name="input_bam" value="3.bam" ftype="bam" />
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<!-- This output tests setting using bam reference name metadata above -->
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<param name="ref_names" value="chr10_random,chr11,chrM,chrX,chr16" />
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<output name="output_of_input_metadata" ftype="txt">
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<assert_contents>
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<has_line line="chr10_random,chr11,chrM,chrX,chr16" />
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</assert_contents>
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</output>
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</test>
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</tests></tool>
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