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comparison varscan_copynumber.xml @ 0:a584f046e4a7 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 13:36:24 -0400
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-1:000000000000 0:a584f046e4a7
1 <tool id="varscan_copynumber" name="VarScan copynumber" version="@VERSION@.0">
2 <description>Determine relative tumor copy number 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
10 varscan copynumber
11 '${normal_pileup}'
12 '${tumor_pileup}'
13 galaxy_out
14 --min-coverage ${min_coverage}
15 --min-base-qual ${min_base_qual}
16 --min-map-qual ${min_map_qual}
17
18 --min-segment-size ${min_segment_size}
19 --max-segment-size ${max_segment_size}
20 --p-value ${p_value}
21 --data-ratio ${data_ratio}
22
23 ]]></command>
24
25 <inputs>
26 <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
27 <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
28
29 <param argument="--min-coverage" name="min_coverage" type="integer" value="20" min="1" max="200"
30 label="Minimum read depth" help="Minimum coverage threshold for copynumber segments"/>
31
32 <param argument="--min-base-qual" name="min_base_qual" type="integer" value="20" min="1" max="200"
33 label="Minimum base quality to count for coverage"/>
34 <param argument="--min-map-qual" name="min_map_qual" type="integer" value="20" min="1" max="200"
35 label="Minimum read mapping quality to count for coverage"/>
36
37 <param argument="--min-segment-size" name="min_segment_size" type="integer" value="10" min="1" max="200"
38 label="Minimum number of consecutive bases to report a segment" help="" />
39 <param argument="--max-segment-size" name="max_segment_size" type="integer" value="100" min="1" max="200"
40 label="Max size before a new segment is made" help="" />
41
42 <expand macro="p_value" label="P-value threshold for significant copynumber change-point" value="0.01" />
43
44 <param argument="--data-ratio" name="data_ratio" type="float" value="1.0" min="0.0" max="1.0"
45 label="The normal/tumor input data ratio for copynumber adjustment"/>
46
47 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
48
49 </inputs>
50 <outputs>
51 <data name="output" from_work_dir="galaxy_out.copynumber" format="interval"/>
52 </outputs>
53 <tests>
54 <test>
55 <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
56 <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
57 <output name="output" file="varscan_copynumber_result1.interval" lines_diff="0" />
58 </test>
59 </tests>
60
61 <help>
62 **VarScan Overview**
63
64 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data.
65 It calls variants from a mpileup dataset and produces a VCF 4.1. Full documentation is available online_.
66
67 This tool estimates the relative tumor copy number from tumor-normal pileups.
68
69 .. _VarScan: http://dkoboldt.github.io/varscan/
70 .. _online: http://dkoboldt.github.io/varscan/using-varscan.html
71
72 **Input**
73
74 ::
75
76 mpileup file - The SAMtools mpileup files for the normal and tumor tissue
77
78
79 **Output**
80
81 VarScan produces a VCF 4.1 dataset as output.
82
83
84 </help>
85 <expand macro="citations" />
86 </tool>