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Imported from capsule None
author anton
date Wed, 11 Jun 2014 17:10:31 -0400
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1 <tool id="vcfsort" name="VCFsort:" version="0.0.1">
2 <description>Sort VCF dataset by coordinate</description>
3 <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"</command>
4 <inputs>
5 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
6 </inputs>
7 <outputs>
8 <data format="vcf" name="out_file1" />
9 </outputs>
10 <tests>
11 <test>
12 <param name="input1" value="vcfsort-test1-input.vcf"/>
13 <output name="out_file1" file="vcfsort-test1.vcf"/>
14 </test>
15 </tests>
16 <help>
17
18 This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is::
19
20 (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file
21
22 .. class:: infomark
23
24 The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order).
25
26 </help>
27 </tool>