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comparison varscan_mpileup.xml @ 0:1e667badbe87 draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797
author iuc
date Tue, 10 Jul 2018 13:36:03 -0400
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1 <tool id="varscan_mpileup" name="VarScan mpileup" version="@VERSION@.0">
2 <description>for variant detection</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command><![CDATA[
9 ## Set up samples list file.
10 #if $sample_names.strip() != '':
11 echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt &&
12 #end if
13
14 ## Set up command + input.
15 varscan ${cmd} '${input}'
16 --min-coverage ${min_coverage}
17 --min-reads2 ${min_reads2}
18 --min-avg-qual ${min_avg_qual}
19 --min-var-freq ${min_var_freq}
20 --min-freq-for-hom ${min_freq_for_hom}
21 --p-value ${p_value}
22
23 #if str($strand_filter) == 'yes':
24 --strand-filter 1
25 #end if
26
27 ## Report only variants in consensus.
28 #if str($cmd) == 'mpileup2cns':
29 --variants
30 #end if
31
32 ## Set up outputs.
33 --output-vcf 1 > '$output'
34
35 #if $sample_names.strip() != '':
36 --vcf-sample-list samples_list.txt
37 #end if
38
39 ]]></command>
40 <inputs>
41 <param name="input" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
42
43 <param name="cmd" type="select" label="Analysis type">
44 <option value="mpileup2snp" selected="True">single nucleotide variation</option>
45 <option value="mpileup2indel">insertions and deletions</option>
46 <option value="mpileup2cns">consensus genotype</option>
47 </param>
48
49 <expand macro="min_coverage" />
50 <expand macro="min_reads2" />
51 <expand macro="min_avg_qual" />
52 <expand macro="min_var_freq" value="0.01" />
53 <expand macro="min_freq_for_hom" />
54 <expand macro="p_value" value="0.99" label="Default p-value threshold for calling variants"/>
55 <expand macro="strand_filter" />
56 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
57 </inputs>
58 <outputs>
59 <data name="output" format="vcf"/>
60 </outputs>
61 <tests>
62 <test>
63 <param name="input" value="test_in1.pileup" />
64 <param name="cmd" value="mpileup2cns" />
65 <param name="min_coverage" value="8" />
66 <param name="min_reads2" value="2" />
67 <param name="min_avg_qual" value="15" />
68 <param name="min_var_freq" value="0.01" />
69 <param name="min_freq_for_hom" value="0.75" />
70 <param name="p_value" value="0.99" />
71 <param name="strand_filter" value="no" />
72 <param name="sample_names" value="" />
73 <output name="output" file="varscan_mpileup_result1.vcf" lines_diff="0" />
74 </test>
75 </tests>
76
77 <help>
78 **VarScan Overview**
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
88 **Input**
89
90 ::
91
92 mpileup file - The SAMtools mpileup file
93
94
95 **Output**
96
97 VarScan produces a VCF 4.1 dataset as output.
98
99 </help>
100 <expand macro="citations" />
101 </tool>