Mercurial > repos > geert-vandeweyer > varscan_wrapper
diff varscan_somatic.xml @ 4:572397bbe057 draft default tip
Added Xmx10G setting to both varscan_somatic wrappers
| author | geert-vandeweyer |
|---|---|
| date | Wed, 26 Mar 2014 05:24:22 -0400 |
| parents | b2ad469e0ff9 |
| children |
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--- a/varscan_somatic.xml Tue Mar 11 06:11:19 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,140 +0,0 @@ -<tool id="varscan_somatic_vcf" name="VarScan Somatic (VCF Output)" version="2.3.5"> - <description> - somatic mutation caller for cancer genomics - </description> - <requirements> - <requirement type="package" version="2.3.5">VarScan</requirement> - </requirements> - <command interpreter="perl"> - - varscan_somatic.pl - "COMMAND::java -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic" - "NORMAL::$normal" - "TUMOR::$tumor" - "TUMORBAM::$tumorbam" - "OUTPUT::$output" - "LOG::$log" - - "OPTION::--min-coverage $min_coverage" - "OPTION::--min-coverage-normal $min_coverage_normal" - "OPTION::--min-coverage-tumor $min_coverage_tumor" - - "OPTION::--min-var-freq $min_var_freq" - "OPTION::--min-freq-for-hom $min_freq_for_hom" - - "OPTION::--normal-purity $normal_purity" - "OPTION::--tumor-purity $tumor_purity" - - "OPTION::--p-value $p_value" - "OPTION::--somatic-p-value $somatic_p_value" - - "OPTION::--strand-filter $strand_filter" - "OPTION::--validation $validation" - "OPTION::--output-vcf 1" - - - - </command> - - <inputs> - - <param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" /> - <param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" /> - <param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" /> - - <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/> - <param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/> - <param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/> - - <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/> - <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/> - - <param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/> - <param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/> - - - <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/> - <param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/> - - <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/> - <param name="validation" type="integer" label="validation" help="" optional="true" value="0"/> - - </inputs> - <outputs> - <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/> - <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/> - <!--<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP file)" /> - <data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL file)" />--> - - - </outputs> - - <help> - -.. class:: infomark - -**What it does** - -:: - - 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. It can be used to detect different types of variation: - - Germline variants (SNPs an dindels) in individual samples or pools of samples. - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup). - Somatic mutations, LOH events, and germline variants in tumor-normal pairs. - Somatic copy number alterations (CNAs) in tumor-normal exome data. - - -**Input** - -:: - - mpileup normal file - The SAMtools mpileup file for normal - mpileup tumor file - The SAMtools mpileup file for tumor - - -**Parameters** - -:: - - min-coverage - Minimum read depth at a position to make a call [8] - - min-coverage-normal - Minimum coverage in normal to call somatic [8] - - min-coverage-tumor - Minimum coverage in tumor to call somatic [6] - - min-var-freq - Minimum variant frequency to call a heterozygote [0.10] - - min-freq-for-hom - Minimum frequency to call homozygote [0.75] - - normal-purity - Estimated purity (non-tumor content) of normal sample [1.00] - - tumor-purity - Estimated purity (tumor content) of tumor sample [1.00] - - p-value - Default p-value threshold for calling variants [0.99] - - somatic-p-value - P-value threshold to call a somatic site [0.05] - - strand-filter - If set to 1, removes variants with >90% strand bias - - validation - If set to 1, outputs all compared positions even if non-variant - - output-vcf - If set to 1, outputs in VCF format [Default] - - - - </help> -</tool> -