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comparison samtools_sort.xml @ 8:71d5c34fef4e draft

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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
comparison
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7:4ab677d8c0de 8:71d5c34fef4e
1 <tool id="samtools_sort" name="Sort" version="2.0"> 1 <tool id="samtools_sort" name="Sort" version="2.0.1">
2 <description>BAM dataset</description> 2 <description>order of storing aligned sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio"></expand> 7 <expand macro="stdio"/>
8 <expand macro="version_command"></expand> 8 <expand macro="version_command"/>
9 <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command> 9 <command><![CDATA[
10 samtools sort
11 $sort_mode
12 -@ \${GALAXY_SLOTS:-1}
13 -o '${output1}'
14 -O bam
15 -T dataset
16 '${input1}'
17 ]]></command>
10 <inputs> 18 <inputs>
11 <param name="input1" type="data" format="bam" label="BAM File" /> 19 <param name="input1" type="data" format="bam" label="BAM File" />
12 <param name="sort_mode" type="select" label="Sort by "> 20 <param name="sort_mode" type="select" label="Sort by ">
13 <option value="" selected="True">Chromosomal coordinates</option> 21 <option value="" selected="True">Chromosomal coordinates</option>
14 <option value="-n">Read names (-n)</option> 22 <option value="-n">Read names (-n)</option>
27 <param name="sort_mode" value="-n"/> 35 <param name="sort_mode" value="-n"/>
28 <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/> 36 <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/>
29 </test> 37 </test>
30 </tests> 38 </tests>
31 <help> 39 <help>
32
33 **What it does** 40 **What it does**
34 41
35 This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order. 42 This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
36
37
38 </help> 43 </help>
39 <expand macro="citations"></expand> 44 <expand macro="citations"/>
40 </tool> 45 </tool>