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+ − 1 <tool id="varscan_pileup" name="VarScan pileup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+ − 2 <description>for variant detection</description>
+ − 3 <macros>
+ − 4 <import>macros.xml</import>
+ − 5 </macros>
+ − 6 <expand macro="requirements"/>
+ − 7 <command detect_errors="exit_code"><![CDATA[
+ − 8 varscan ${cmd} '${input}'
+ − 9 --min-coverage ${min_coverage}
+ − 10 --min-reads2 ${min_reads2}
+ − 11 --min-avg-qual ${min_avg_qual}
+ − 12 --min-var-freq ${min_var_freq}
+ − 13 --min-freq-for-hom ${min_freq_for_hom}
+ − 14 --p-value ${p_value}
+ − 15 --output-vcf 1 > '$output'
+ − 16 ]]></command>
+ − 17 <inputs>
+ − 18 <param name="input" format="pileup" type="data" label="Samtools pileup file"/>
+ − 19 <param name="cmd" type="select" label="Analysis type">
+ − 20 <option value="pileup2snp" selected="True">Identify SNPs from a pileup file</option>
+ − 21 <option value="pileup2indel">Identify indels a pileup file</option>
+ − 22 <option value="pileup2cns">Call consensus and variants from a pileup file</option>
+ − 23 </param>
+ − 24 <param argument="--min-coverage" type="integer" value="8" min="1" max="200" label="Minimum coverage"/>
+ − 25 <param argument="--min-reads2" type="integer" value="2" min="1" max="200" label="Minimum supporting reads"/>
+ − 26 <param argument="--min-avg-qual" type="integer" value="15" min="1" max="50" label="Minimum base quality" help="The minimum base quality at the variant position required to use a read for calling"/>
+ − 27 <param argument="--min-var-freq" type="float" value="0.01" min="0" max="1" label="Minimum variant allele frequency" help="Minimum variant allele frequency required for calling a variant"/>
+ − 28 <param argument="--min-freq-for-hom" type="float" value="0.75" min="0" max="1" label="Minimum homozygous variant allele frequency" help="Minimum variant allele frequency (default: 0.75) required for calling a homozygous genotype"/>
+ − 29 <param argument="--p-value" type="float" value="0.01" min="0" max="1" label="Default p-value threshold for calling variants"/>
+ − 30 </inputs>
+ − 31 <outputs>
+ − 32 <data name="output" format="vcf"/>
+ − 33 </outputs>
+ − 34 <tests>
+ − 35 <test>
+ − 36 <param name="input" value="input1.pileup"/>
+ − 37 <param name="cmd" value="pileup2snp"/>
+ − 38 <param name="min_coverage" value="15"/>
+ − 39 <param name="min_avg_qual" value="15"/>
+ − 40 <param name="min_var_freq" value="0.8"/>
+ − 41 <param name="p_value" value="0.01"/>
+ − 42 <output name="output" file="output1.vcf" ftype="vcf"/>
+ − 43 </test>
+ − 44 </tests>
+ − 45
+ − 46 <help><![CDATA[
+ − 47 **VarScan Overview**
+ − 48
+ − 49 VarScan_ performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. Full documentation of the command line package is available here_.
+ − 50
+ − 51 .. _VarScan: http://dkoboldt.github.io/varscan/
+ − 52 .. _here: http://dkoboldt.github.io/varscan/using-varscan.html
+ − 53
+ − 54 **Input**
+ − 55
+ − 56 ::
+ − 57
+ − 58 pileup file - The SAMtools pileup file
+ − 59
+ − 60 **Output**
+ − 61
+ − 62 VarScan produces a VCF dataset as output.
+ − 63 ]]></help>
+ − 64 <expand macro="citations"/>
+ − 65 </tool>