Mercurial > repos > jbrayet > samtools_sort_docker
changeset 5:e95f34f52fc8 draft
Uploaded
author | jbrayet |
---|---|
date | Wed, 18 Nov 2015 06:58:13 -0500 |
parents | 6024acc63f80 |
children | b2d324e394ac |
files | samtools_sort.xml |
diffstat | 1 files changed, 4 insertions(+), 10 deletions(-) [+] |
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--- a/samtools_sort.xml Wed Nov 18 06:57:38 2015 -0500 +++ b/samtools_sort.xml Wed Nov 18 06:58:13 2015 -0500 @@ -1,11 +1,9 @@ <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> + <requirements> + <requirement type="package" version="0.1">docker_samtools</requirement> + <container type="docker">samtools:1.0</container> + </requirements> <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" /> @@ -17,14 +15,10 @@ <outputs> <data name="output1" format="bam" /> </outputs> - <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>