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sort_bam.xml
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sort_bam.xml
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<tool id="sort_bam" name="sort_bam" version="1.1">
<description>Sort bam file based on chromosomal coordinates.</description>
<requirements>
<requirement type="set_environment">LINKYX_PATH</requirement>
<requirement type="set_environment">SAMTOOLS</requirement>
<requirement type="package" version="0.1.19">samtools-fpic</requirement>
<requirement type="package" version="1.6.922">bioperl</requirement>
</requirements>
<command interpreter="bash">sort_bam.sh $output $input1</command>
<inputs>
<param format="bam" name="input1" type="data" label="Alignment file"/>
</inputs>
<outputs>
<data format="bam" name="output" />
</outputs>
<tests>
<test>
</test>
</tests>
<help>
Sort bam file based on chromosomal coordinates.
</help>
</tool>