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comparison vcffilter.xml @ 1:e5dd21db760b draft

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author anton
date Mon, 12 May 2014 15:53:18 -0400
parents c56b2e440fce
children 77e44d465705
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0:c56b2e440fce 1:e5dd21db760b
1 <tool id="vcffilter" name="VCFfilter:" version="0.0.1"> 1 <tool id="vcffilter" name="VCFfilter:" version="0.0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement> 3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
4 </requirements> 4 </requirements>
5 <description>filter VCF data in a variety of attributes</description> 5 <description>filter VCF data in a variety of attributes</description>
6 <command>vcffilter ${filterList} "${input}" > "${out_file1}"</command> 6 <command>
7 <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg -->
8 ln -s "${input1}" input1.vcf.gz &amp;&amp;
9 ln -s "${Tabixized_input}" input1.vcf.gz.tbi &amp;&amp;
10 vcffilter ${filterList} input1.vcf.gz > "${out_file1}"
11 </command>
12
7 <inputs> 13 <inputs>
8 <param name="filterList" size="40" type="text" value="-f &quot;DP &gt; 10&quot;" label="Specify filterting expression" help="See explanation of filtering options below"> 14 <param name="filterList" size="40" type="text" value="-f &quot;DP &gt; 10&quot;" label="Specify filterting expression" help="See explanation of filtering options below">
9 <sanitizer> 15 <sanitizer>
10 <valid initial="string.printable"> 16 <valid initial="string.printable">
11 <remove value="&apos;"/> 17 <remove value="&apos;"/>
12 </valid> 18 </valid>
13 <mapping initial="none"> 19 <mapping initial="none">
14 <add source="&apos;" target="__sq__"/> 20 <add source="&apos;" target="__sq__"/>
15 </mapping> 21 </mapping>
16 </sanitizer> 22 </sanitizer>
17 </param> 23 </param>
18 <param format="vcf" name="input" type="data" label="From"/> 24 <param format="vcf_bgzip" name="input1" type="data" label="From">
25 <conversion name="Tabixized_input" type="tabix" />
26 </param>
19 </inputs> 27 </inputs>
20 <outputs> 28 <outputs>
21 <data format="vcf" name="out_file1" /> 29 <data format="vcf" name="out_file1" />
22 </outputs> 30 </outputs>
23 <tests> 31 <tests>
24 <test> 32 <test>
25 <param name="filterList" value="-f &quot;DP &gt; 10&quot;"/> 33 <param name="filterList" value="-f &quot;DP &gt; 10&quot;"/>
26 <param name="input" value="vcflib.vcf"/> 34 <param name="input1" value="vcflib.vcf"/>
27 <output name="out_file1" file="vcffilter-test1.vcf"/> 35 <output name="out_file1" file="vcffilter-test1.vcf"/>
28 </test> 36 </test>
29 </tests> 37 </tests>
30 <help> 38 <help>
31 39
32 VCFfilter is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). 40 VCFfilter is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
33 41
34 You can specify the following option the **Specify filtering expression** box in any combination:: 42 You can specify the following option the **Specify filtering expression** box in any combination::
35 43