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comparison varscan_mpileup.xml @ 2:89702e7ec3c3 draft

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author devteam
date Sat, 16 Nov 2013 18:48:12 -0500
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1 <tool id="varscan" name="Varscan" version="0.1">
2 <description>for variant detection</description>
3
4 <requirements>
5 <requirement type="package" version="2.3.6">varscan</requirement>
6 </requirements>
7
8 <!--
9 The version command string is not yet a template that can be filled in, so version command is not yet possible.
10 <version_command>java -jar ${GALAXY_DATA_INDEX_DIR}/shared/jars/varscan/VarScan.jar 2>&amp;1 | head -n 1</version_command>
11 -->
12
13 <command>
14 ## Set up samples list file.
15 #if $sample_names.strip() != '':
16 echo $sample_names | awk -F ',' '{ for (i = 1; i &lt;= NF; i++) { print \$i; } }' > samples_list.txt;
17 #end if
18
19 ## Set up command + input.
20 java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar ${cmd} ${input}
21 --min-coverage ${min_coverage}
22 --min-reads2 ${min_supporting_reads}
23 --min-avg-qual ${min_avg_qual}
24 --min-var-freq ${min_var_freq}
25 --min-freq-for-hom ${min_freq_for_hom}
26 --p-value ${p_value}
27 #if str($strand_filter) == 'yes':
28 --strand-filter 1
29 #end if
30
31 ## Report only variants in consensus.
32 #if str($cmd) == 'mpileup2cns':
33 --variants
34 #end if
35
36 ## Set up outputs.
37 --output-vcf 1 > $output
38
39 #if $sample_names.strip() != '':
40 --vcf-sample-list samples_list.txt
41 #end if
42 </command>
43
44 <inputs>
45 <param format="pileup" name="input" type="data" label="Pileup dataset" help=""/>
46
47 <param name="cmd" type="select" label="Analysis type">
48 <option value="mpileup2snp" selected="True">single nucleotide variation</option>
49 <option value="mpileup2indel">insertions and deletions</option>
50 <option value="mpileup2cns">consensus genotype</option>
51 </param>
52
53 <param name="min_coverage" type="integer" value="8" min="1" max="200" label="Minimum read depth" help="Minimum depth at a position to make a call"/>
54 <param name="min_supporting_reads" type="integer" value="2" min="1" max="200" label="Minimum supporting reads" help="Minimum supporting reads at a position to make a call"/>
55 <param name="min_avg_qual" type="integer" value="15" min="1" max="50" label="Minimum base quality at a position to count a read"/>
56 <param name="min_var_freq" type="float" value="0.01" min="0" max="1" label="Minimum variant allele frequency threshold"/>
57 <param name="min_freq_for_hom" type="float" value="0.75" min="0" max="1" label="Minimum frequency to call homozygote"/>
58 <param name="p_value" type="float" value="0.99" min="0" max="1" label="p-value threshold for calling variants"/>
59 <param name="strand_filter" type="select" label="Ignore variants with >90% support on one strand">
60 <option value="no" selected="True">no</option>
61 <option value="yes">yes</option>
62 </param>
63 <param name="sample_names" type="text" value="" help="Separate sample names by comma; leave blank to use default sample names."/>
64 </inputs>
65
66 <stdio>
67 <regex match="Exception" source="both" level="fatal" description="Tool exception"/>
68 <regex match=".*" source="both" level="log" description="tool progress"/>
69 </stdio>
70
71 <outputs>
72 <data name="output" format="vcf"/>
73 </outputs>
74
75 <trackster_conf>
76 </trackster_conf>
77
78 <tests>
79 <test>
80 <param name="input" value="test_in1.pileup" />
81 <param name="cmd" value="mpileup2cns" />
82 <param name="min_coverage" value="8" />
83 <param name="min_supporting_reads" value="2" />
84 <param name="min_avg_qual" value="15" />
85 <param name="min_var_freq" value="0.01" />
86 <param name="min_freq_for_hom" value="0.75" />
87 <param name="p_value" value="0.99" />
88 <param name="strand_filter" value="no" />
89 <param name="sample_names" value="" />
90 <output name="output" file="test_out1.vcf" lines_diff="0" />
91 </test>
92 </tests>
93
94 <help>
95 **VarScan Overview**
96
97 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1 Full documentation is available online_.
98
99 Please cite: Koboldt, D., Zhang, Q., Larson, D., Shen, D., McLellan, M., Lin, L., Miller, C., Mardis, E., Ding, L., and Wilson, R. (2012). VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Research DOI: 10.1101/gr.129684.111
100
101 .. _VarScan: http://varscan.sourceforge.net/
102 .. _online: http://varscan.sourceforge.net/using-varscan.html
103
104 **Input**
105
106 ::
107
108 mpileup file - The SAMtools mpileup file
109
110
111 **Output**
112
113 VarScan produces a VCF 4.1 dataset as output.
114
115 **Parameters**
116
117 ::
118
119 analysis type
120 single nucleotide detection Identify SNPs from an mpileup file
121 insertions and deletion Identify indels an mpileup file
122 consensus genotype Call consensus and variants from an mpileup file
123
124 min-coverage
125 Minimum read depth at a position to make a call [8]
126
127 min-reads2
128 Minimum supporting reads at a position to call variants [2]
129
130 min-avg-qual
131 Minimum base quality at a position to count a read [15]
132
133 min-var-freq
134 Minimum variant allele frequency threshold [0.01]
135
136 min-freq-for-hom
137 Minimum frequency to call homozygote [0.75]
138
139 p-value
140 Default p-value threshold for calling variants [99e-02]
141
142 strand-filter
143 Ignore variants with >90% support on one strand [1]
144
145 output-vcf
146 If set to 1, outputs in VCF format
147
148 vcf-sample-list
149 For VCF output, a list of sample names in order, one per line
150
151 variants
152 Report only variant (SNP/indel) positions [0]
153
154 </help>
155 </tool>