Mercurial > repos > iuc > varscan_mpileup

comparison varscan_mpileup.xml @ 2:d062703d6f13 draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
author iuc
date Tue, 04 Dec 2018 05:16:18 -0500
parents 1e667badbe87
children
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1:0bc800d67a0e 2:d062703d6f13
1 <tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.0"> 1 <tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.1">
2 <description>for variant detection</description> 2 <description>for variant detection</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements">
7 <requirement type="package" version="4.2.1">gawk</requirement>
8 </expand>
7 <expand macro="stdio" /> 9 <expand macro="stdio" />
8 <command><![CDATA[ 10 <command><![CDATA[
9 ## Set up samples list file. 11 ## Set up samples list file.
10 #if $sample_names.strip() != '': 12 #if $sample_names.strip() != '':
11 echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt && 13 echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt &&
72 <param name="sample_names" value="" /> 74 <param name="sample_names" value="" />
73 <output name="output" file="varscan_mpileup_result1.vcf" lines_diff="0" /> 75 <output name="output" file="varscan_mpileup_result1.vcf" lines_diff="0" />
74 </test> 76 </test>
75 </tests> 77 </tests>
76 78
77 <help> 79 <help><![CDATA[
78 **VarScan Overview** 80 @HELP_HEADER@
79
80 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
81 It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
82
83 This tool detects variants from pileups.
84
85 .. _VarScan: http://dkoboldt.github.io/varscan/
86 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html
87 81
88 **Input** 82 **Input**
89 83
90 :: 84 ::
91 85
94 88
95 **Output** 89 **Output**
96 90
97 VarScan produces a VCF 4.1 dataset as output. 91 VarScan produces a VCF 4.1 dataset as output.
98 92
99 </help> 93 ]]></help>
100 <expand macro="citations" /> 94 <expand macro="citations" />
101 </tool> 95 </tool>