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comparison vcfsort.xml @ 3:5b7120c66efc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
author iuc
date Mon, 26 Mar 2018 12:28:53 -0400
parents a8c5440d69e3
children f0580efedada
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2:a8c5440d69e3 3:5b7120c66efc
1 <tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@.0"> 1 <tool id="vcfsort" name="VCFsort:" version="@WRAPPER_VERSION@+galaxy0">
2 <description>Sort VCF dataset by coordinate</description> 2 <description>Sort VCF dataset by coordinate</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <command>(grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"</command> 6 <command><![CDATA[
7 <inputs> 7 (grep ^"#" "${input1}" && grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}"
8 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> 8 ]]></command>
9 </inputs> 9 <inputs>
10 <outputs> 10 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/>
11 <data format="vcf" name="out_file1" /> 11 </inputs>
12 </outputs> 12 <outputs>
13 <tests> 13 <data format="vcf" name="out_file1" />
14 <test> 14 </outputs>
15 <param name="input1" value="vcfsort-test1-input.vcf"/> 15 <tests>
16 <output name="out_file1" file="vcfsort-test1.vcf"/> 16 <test>
17 </test> 17 <param name="input1" value="vcfsort-test1-input.vcf"/>
18 <output name="out_file1" file="vcfsort-test1.vcf"/>
19 </test>
18 </tests> 20 </tests>
19 <help> 21 <help>
20
21 This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is:: 22 This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is::
22 23
23 (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file 24 (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file
24 25
25 .. class:: infomark 26 .. class:: infomark
26 27
27 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). 28 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).
28 29 </help>
29 </help>
30 </tool> 30 </tool>