comparison varscan_mpileup2indel.xml @ 0:10e2ea79ec55 draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
author yhoogstrate
date Thu, 05 Nov 2015 10:00:19 -0500
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children 2c56a59a112f
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1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="varscan_mpileup2indel" name="VarScan2 Call INDELs from a mpileup file" version="2.3.6.a">
3 <description>VarScan2 INDEL detection; directly from a *.mpileup file.</description>
4
5 <requirements>
6 <requirement type="package" version="2.3.6">varscan</requirement>
7 </requirements>
8
9 <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&amp;1 | head -n 1</version_command>
10
11 <command>
12 cat $mpileup_input | java
13 -Xmx64G
14 -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
15 mpileup2indel
16
17 #if $extended_parameters.parameters == "extended"
18 --min-coverage $extended_parameters.varscan_min_coverage
19 --min-reads2 $extended_parameters.varscan_min_reads2
20 --min-avg-qual $extended_parameters.varscan_min_avg_qual
21 --min-var-freq $extended_parameters.varscan_min_var_freq
22 --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
23 --p-value $extended_parameters.varscan_p_value
24 $extended_parameters.varscan_strand_filter
25 $extended_parameters.varscan_variants
26 #end if
27
28 #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
29 --output-vcf 1
30 #end if
31
32 2> stderr.txt
33 > $snv_output ;
34 cat stderr.txt
35 </command>
36
37 <inputs>
38 <param format="pileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/><!-- datatype "mpileup" does not exist.. it seems to be common to use pileup instead? -->
39
40 <conditional name="extended_parameters">
41 <param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings.">
42 <option value="default">Default settings</option>
43 <option value="extended">Extended settings</option>
44 </param>
45 <when value="default">
46 </when>
47 <when value="extended">
48 <param type="integer" name="varscan_min_coverage" value="8" label="VarScan: Minimum read depth at a position to make a call [8]" />
49 <param type="integer" name="varscan_min_reads2" value="2" label="VarScan: PMinimum supporting reads at a position to call variants [2]" />
50 <param type="integer" name="varscan_min_avg_qual" value="15" label="VarScan: Minimum base quality at a position to count a read [15]" />
51 <param type="float" name="varscan_min_var_freq" value="0.01" label="VarScan: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" />
52 <param type="float" name="varscan_min_freq_for_hom" value="0.75" label="VarScan: Minimum frequency to call homozygote [0.75]" />
53 <param type="float" name="varscan_p_value" value="0.99" label="VarScan: Default p-value threshold for calling variants [99e-02]" />
54 <param type="boolean" name="varscan_strand_filter" falsevalue=" --strand_filter 0" truevalue=" --strand_filter 1" checked="true" label="VarScan: Ignore variants with >90% support on one strand [1]" />
55 <param type="boolean" name="varscan_variants" falsevalue=" --variants 0" truevalue=" --variants 1" checked="false" label="VarScan: Report only variant (SNP/indel) positions [0]" />
56 </when>
57 </conditional>
58
59 <param name="varscan_output" type="select" label="Output format">
60 <option value="vcf">VCF</option>
61 <option value="tabular">tabular</option>
62 </param>
63 </inputs>
64
65 <outputs>
66 <data format="tabular" name="snv_output" label="${tool.name} on ${mpileup_input.hid}: ${mpileup_input.name}">
67 <change_format>
68 <when input="varscan_output" value="vcf" format="vcf" />
69 </change_format>
70 </data>
71 </outputs>
72
73 <tests>
74 <test>
75 <param name="mpileup_input" value="example.mpileup" ftype="pileup" />
76 <param name="parameters" value="default" />
77 <param name="varscan_output_vcf" value="1" />
78
79 <output name="snv_output" file="example.vcf" />
80 </test>
81 </tests>
82
83 <help>
84 **VarScan 2.3.6**
85
86 VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems.
87 http://dx.doi.org/10.1101/gr.129684.111
88 http://www.ncbi.nlm.nih.gov/pubmed/19542151
89
90 *VarScan* requires mpileup formatted input files, which are generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing it is bypassed. Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan.
91 The samtools package is not able to parallelize the mpileup generation which make it a very slow process.
92 Other people were aware of this and have written a version that can do parallelization:
93 https://github.com/mydatascience/parallel-mpileup
94
95 Consequently, when a BAM files gets processed by this wrapper, it's processed by *parallel-mpileup* before its send to VarScan.
96
97 .. _VarScan: http://varscan.sourceforge.net/
98
99 **Input formats**
100
101 VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing.
102
103 **Installation**
104
105 Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment.
106
107 **License**
108
109 * VarScan2.3.6: Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0)
110 * parallel-mpileup: MIT License (https://github.com/mydatascience/parallel-mpileup/blob/master/samtools-0.1.19/COPYING)
111
112 Contact
113 -------
114
115 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
116 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
117 Research IT (TraIT) project:
118
119 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
120
121 More tools by the Translational Research IT (TraIT) project can be found
122 in the following toolsheds:
123
124 http://toolshed.g2.bx.psu.edu/
125
126 http://testtoolshed.g2.bx.psu.edu/
127 </help>
128 <citations>
129 <citation type="doi">10.1101/gr.129684.111</citation>
130 </citations>
131 </tool>