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comparison samtools_sort.xml @ 5:346239545aa0 draft

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Uploaded tool xml with improved command line.
author devteam
date Thu, 16 Oct 2014 12:42:20 -0400
parents 1d317aeacef4
children 191cec7b989b
comparison
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4:1d317aeacef4 5:346239545aa0
1 <tool id="samtools_sort" name="sort" version="1.0.3"> 1 <tool id="samtools_sort" name="sort" version="1.0.3">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.1">samtools</requirement> 3 <requirement type="package" version="1.1">samtools</requirement>
4 </requirements> 4 </requirements>
5 <description>a BAM file</description> 5 <description>a BAM file</description>
6 <command> 6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
7 samtools sort 7 <command>samtools sort $sort_mode "${input1}" -o "${output1}" -O bam -T dataset</command>
8 $sort_mode 8 <stdio>
9 "${input1}" foo 9 <exit_code range="1:" level="fatal" description="Error" />
10 2&gt;&amp;1 || echo "Error running samtools sort." &gt;&amp;2 10 </stdio>
11 ;
12 mv foo.bam "${output1}"
13 </command>
14 <inputs> 11 <inputs>
15 <param name="input1" type="data" format="bam" label="BAM File" /> 12 <param name="input1" type="data" format="bam" label="BAM File" />
16 <param name="sort_mode" type="select" label="Sort by "> 13 <param name="sort_mode" type="select" label="Sort by ">
17 <option value="" selected="True">Chromosomal coordinates</option> 14 <option value="" selected="True">Chromosomal coordinates</option>
18 <option value="-n">Read names</option> 15 <option value="-n">Read names</option>