Mercurial > repos > devteam > samtools_sort
diff samtools_sort.xml @ 0:a430da4f04cd draft
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author | devteam |
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date | Tue, 21 Apr 2015 17:41:18 -0400 |
parents | |
children | cab3f8d35989 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_sort.xml Tue Apr 21 17:41:18 2015 -0400 @@ -0,0 +1,40 @@ +<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>