Mercurial > repos > devteam > samtools_sort
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author | devteam |
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date | Tue, 21 Apr 2015 17:41:18 -0400 |
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children | cab3f8d35989 |
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<tool id="samtools_sort" name="Sort" version="2.0"> <description>BAM dataset</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"></expand> <expand macro="stdio"></expand> <expand macro="version_command"></expand> <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command> <inputs> <param name="input1" type="data" format="bam" label="BAM File" /> <param name="sort_mode" type="select" label="Sort by "> <option value="" selected="True">Chromosomal coordinates</option> <option value="-n">Read names (-n)</option> </param> </inputs> <outputs> <data name="output1" format="bam" /> </outputs> <tests> <test> <param name="input1" value="1.bam" ftype="bam" /> <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/> </test> <test> <param name="input1" value="1.bam" ftype="bam" /> <param name="sort_mode" value="-n"/> <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/> </test> </tests> <help> **What it does** This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order. </help> <expand macro="citations"></expand> </tool>