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comparison samtools_sort.xml @ 9:33ed69baef65 draft default tip

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author jbrayet
date Wed, 18 Nov 2015 09:11:05 -0500
parents b499934c6780
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8:b499934c6780 9:33ed69baef65
1 <tool id="samtools_sort" name="Sort" version="0.1"> 1 <tool id="samtools_sort" name="Sort" version="0.1">
2 <description>BAM dataset</description> 2 <description>BAM dataset</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1">docker_samtools</requirement> 4 <requirement type="package" version="0.1">docker_samtools</requirement>
5 <container type="docker">samtools:1.0</container> 5 <container type="docker">viv1/samtools:1.2</container>
6 </requirements> 6 </requirements>
7 <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command> 7 <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
8 <inputs> 8 <inputs>
9 <param name="input1" type="data" format="bam" label="BAM File" /> 9 <param name="input1" type="data" format="bam" label="BAM File" />
10 <param name="sort_mode" type="select" label="Sort by "> 10 <param name="sort_mode" type="select" label="Sort by ">