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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 13:35:40 -0400
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1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.0">
2 <description>Call germline/somatic variants from tumor-normal pileups</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command><![CDATA[
9 varscan somatic
10 '${normal_pileup}'
11 '${tumor_pileup}'
12 galaxy_out
13 --min-coverage ${min_coverage}
14 --min-reads2 ${min_reads2}
15 --min-avg-qual ${min_avg_qual}
16 --min-var-freq ${min_var_freq}
17 --min-freq-for-hom ${min_freq_for_hom}
18 --normal-purity ${normal_purity}
19 --tumor-purity ${tumor_purity}
20 --tumor-purity ${tumor_purity}
21 --min-coverage-normal ${min_coverage_normal}
22 --somatic-p-value ${somatic_p_value}
23 --p-value ${p_value}
24 #if str($strand_filter) == 'yes':
25 --strand-filter 1
26 #end if
27
28 --output-vcf 1
29 ]]></command>
30
31 <inputs>
32 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
33 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
34
35 <expand macro="min_coverage" />
36 <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200"
37 label="Minimum read depth from the normal sample" help="Minimum depth at a position to make a call" />
38 <param argument="--min-coverage-tumor" name="min_coverage_tumor" type="integer" value="6" min="1" max="200"
39 label="Minimum read depth from the tumor sample" help="Minimum depth at a position to make a call" />
40 <expand macro="min_reads2" />
41 <expand macro="min_avg_qual" />
42 <expand macro="min_var_freq" value="0.10" />
43 <expand macro="min_freq_for_hom" />
44 <param argument="--normal-purity" name="normal_purity" type="float" value="1.00" min="0" max="1.00"
45 label="Estimated purity (non-tumor content) of normal sample"/>
46 <param argument="--tumor-purity" name="tumor_purity" type="float" value="1.00" min="0" max="1.00"
47 label="Estimated purity (tumor content) of tumor sample"/>
48 <expand macro="p_value" label="P-value threshold to call a heterozygote" value="0.99"/>
49 <param argument="--somatic-p-value" name="somatic_p_value" type="float" value="0.05" min="0" max="1"
50 label="p-value threshold for calling somatic sites"/>
51 <expand macro="strand_filter" />
52 </inputs>
53 <outputs>
54 <data name="output_indel" from_work_dir="galaxy_out.indel.vcf" format="vcf"/>
55 <data name="output_snp" from_work_dir="galaxy_out.snp.vcf" format="vcf"/>
56 </outputs>
57 <tests>
58 <test>
59 <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
60 <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
61 <param name="min_coverage" value="2" />
62 <param name="min_coverage_normal" value="2" />
63 <param name="min_coverage_tumor" value="2" />
64 <param name="min_reads2" value="1" />
65 <param name="min_avg_qual" value="5" />
66 <param name="min_var_freq" value="0.01" />
67 <param name="min_freq_for_hom" value="0.75" />
68 <param name="normal_purity" value="0.6" />
69 <param name="tumor_purity" value="0.6" />
70 <param name="p_value" value="0.99" />
71 <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" />
72 <output name="output_snp" file="varscan_somatic_snp_result1.vcf" lines_diff="0" />
73 </test>
74 </tests>
75
76 <help>
77 **VarScan Overview**
78
79 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
80 It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
81
82 This tool calls germline/somatic variants from tumor-normal pileups.
83
84 .. _VarScan: http://dkoboldt.github.io/varscan/
85 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html
86
87 **Input**
88
89 ::
90
91 mpileup file - The SAMtools mpileup files for the normal and tumor tissue
92
93
94 **Output**
95
96 VarScan produces a VCF 4.1 dataset as output.
97
98
99 </help>
100 <expand macro="citations" />
101 </tool>