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mutect.xml
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<tool id="mutect" name="MuTect" version="1.0.0">
<description>identify somatic point mutations</description>
<requirements>
<container type="docker">mutect:1.1.5</container>
</requirements>
<command interpreter="python">mutect.py
--reference-sequence $reference
#if str($cosmic) != "":
--cosmic $cosmic
#end if
#if str($dbsnp) != "":
--dbsnp $dbsnp
#end if
#if str($contamination.input) == "value":
--fraction_contamination $contamination.input_value
#end if
#if str($contamination.input) == "value_file":
--fraction_contamination-file $contamination.input_file
#end if
--tumor_lod ${tumor_lod}
--initial_tumor_lod ${initial_tumor_lod}
--input_file:normal $normal
--input_file:index:normal $normal.metadata.bam_index
--input_file:tumor $tumor
--input_file:index:tumor $tumor.metadata.bam_index
--out call_stats.txt
--coverage_file coverage.wig.txt
--vcf mutations.vcf
--workdir ./
--ncpus \${GALAXY_SLOTS:-4}
</command>
<inputs>
<param name="reference" type="data" format="bed, fasta" label="Select a reference genome"/>
<param name="normal" type="data" format="bam" label="Normal BAM file"/>
<param name="tumor" type="data" format="bam" label="Tumor BAM file"/>
<param name="dbsnp" type="data" format="vcf" label="dbsnp.vcf file" optional="true"/>
<param name="cosmic" type="data" format="vcf" label="Cosmic vcf file" optional="true"/>
<param name="intervals" type="text" label="Intervals to process" help="In format 'chr1:1500-2500; chr2:2500-3500', separated by semicolons" optional="true"/>
<param name="intervalfile" type="data" format="txt" label="Intervals to process (.txt file)" help="'chr1:1500-2500', one entry per line" optional="true"/>
<conditional name="contamination">
<param name="input" type="select" label="Sample Contamination">
<option value="na" selected="True">NA</option>
<option value="value">Value</option>
<option value="value_file">Value File</option>
</param>
<when value="value">
<param name="input_value" type="float" label="Contamination Value" value="0.1"/>
</when>
<when value="value_file">
<param name="input_file" type="data" format="txt" label="Contamination Value File"/>
</when>
</conditional>
<param name="tumor_lod" type="float" label="Tumor LOD" help="LOD threshold for calling tumor variant" value="6.3"/>
<param name="initial_tumor_lod" type="float" label="Tumor LOD" help="Initial LOD threshold for calling tumor variant" value="4.0"/>
</inputs>
<outputs>
<data format="txt" name="callstats" label="MuTect CallsDetailed" from_work_dir="call_stats.txt"/>
<data format="txt" name="coverage" label="MuTect CoverageOutput" from_work_dir="coverage.wig.txt"/>
<data format="vcf" name="mutations" label="MuTect VCF" from_work_dir="mutations.vcf"/>
</outputs>
<stdio>
<exit_code range="1:" level="fatal" />
</stdio>
<help>
.. class:: infomark
**License**
Copyright (c) 2012 The Broad Institute
Please view our documentation at http://www.broadinstitute.org/gsa/wiki
For support, please view our support site at http://getsatisfaction.com/gsa
**What it does**
MuTect is a method developed at the Broad Institute for the reliable
and accurate identification of somatic point mutations in next generation
sequencing data of cancer genomes.
**Input**
Reference Genome:
Fasta file of ref gnome
Normal Sample:
bam normal sample
Tumor Sample:
bam tumor sample
Intervals:
A list of genomic intervals over which to operate.
**Output**
Caller Output:
Detailed caller output
Coverage Output:
write out coverage in WIGGLE format to this file
VCF Output:
VCF output of mutation calls
</help>
</tool>