Mercurial > repos > devteam > samtools_sort
diff samtools_sort.xml @ 8:71d5c34fef4e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
| author | iuc |
|---|---|
| date | Tue, 09 May 2017 11:16:15 -0400 |
| parents | 191cec7b989b |
| children | 17bed26ad17e |
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--- a/samtools_sort.xml Fri Dec 18 19:46:37 2015 -0500 +++ b/samtools_sort.xml Tue May 09 11:16:15 2017 -0400 @@ -1,12 +1,20 @@ -<tool id="samtools_sort" name="Sort" version="2.0"> - <description>BAM dataset</description> +<tool id="samtools_sort" name="Sort" version="2.0.1"> + <description>order of storing aligned sequences</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> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + 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 "> @@ -29,12 +37,9 @@ </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> + <expand macro="citations"/> </tool>