view varscan2_from_bam.xml @ 10:29ac0abd267e

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<?xml version="1.0" encoding="UTF-8"?>
<tool id="varscan2_from_bam" name="VarScan2 from BAM">
	<description>VarScan2 (1: directly reading a *.bam file, 2: using parallel mpileup generation, to avoid unncessairy I/O overhead.</description>
	<requirements>
		<requirement type="package" version="1.0.19">samtools-mpileup-parallel</requirement>
		<requirement type="package" version="2.3.6">VarScan</requirement>
	</requirements>
	<command>
		samtools-mpileup-parallel mpileup
			-t $samtools_threads
			-f $reference_genome
		
		#if $extended_parameters_regions.samtools_regions == "region"
			-r $extended_parameters_regions.$samtools_r
		#elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
			-l $extended_parameters_regions.$samtools_l
		#end if
		
		#if $extended_parameters.parameters == "extended"
			$extended_parameters.samtools_6
			$extended_parameters.samtools_A
			$extended_parameters.samtools_B
			 -C $extended_parameters.samtools_C
			 -d $extended_parameters.samtools_d
			$extended_parameters.samtools_E
			 -M $extended_parameters.samtools_M
			$extended_parameters.samtools_R
			 -q $extended_parameters.samtools_q
			 -Q $extended_parameters.samtools_Q
			
			 -e $extended_parameters.samtools_e
			 -F $extended_parameters.samtools_F
			 -h $extended_parameters.samtools_h
			$extended_parameters.samtools_I
			 -L $extended_parameters.samtools_L
			 -m $extended_parameters.samtools_m
			 -o $extended_parameters.samtools_o
			$extended_parameters.samtools_p
			 -P $extended_parameters.samtools_P
		#end if
		
		#for $sample in $samples
			 ${sample.mapped_reads}
		#end for
		
		 | java
				 -Xmx64G
				 -jar VarScan.v2.3.6.jar
					 mpileup2snp
		 
		#if $extended_parameters.parameters == "extended"
				 --min-coverage     $varscan_min_coverage
				 --min-reads2       $varscan_min_reads2
				 --min-avg-qual     $varscan_min_avg_qual
				 --min-var-freq     $varscan_min_var_freq
				 --min-freq-for-hom $varscan_min_freq_for_hom
				 --p-value          $varscan_p_value
				$varscan_strand_filter
				$varscan_output_vcf
				$varscan_variants
		#end if
		
		$varscan_output_vcf
		 
		 > $output_table
	</command>
	
	<inputs>
		<repeat name="samples" title="Samples" min="1">
			<param format="bam,sam" name="mapped_reads" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/>
		</repeat>
		
		<!-- Find out how to access the reference genome from the BAM file(s) -->
		<param format="fa,fasta" name="reference_genome" type="data" label="Gene Model Annotations" help="Reference genome (genome.fa) that corresponds to the *.bam file." />
		
		<conditional name="extended_parameters_regions">
			<param name="samtools_regions" type="select" label="VarScan parameters" help="For more advanced VarScan settings.">
				<option value="entire_genome">Entire genome</option>
				<option value="region">Specific region</option>
				<option value="regions_file_pos">Specific positions (file); list of positions</option>
				<option value="regions_file_bed">Specific regions (file); list of regions in BED</option>
			</param>
			<when value="entire_genome">
			</when>
			<when value="region">
				<param type="text" name="samtools_r" label="Samtools: region in which pileup is generated" help="chr:pos or chr:start-end" />
			</when>
			<when value="regions_file_pos">
				<param type="data" name="samtools_l" format="tabular" label="Samtools: list of positions (chr pos)" />
			</when>
			<when value="regions_file_bed">
				<param type="data" name="samtools_l" format="bed"     label="Samtools: specific regions (BED)" />
			</when>
		</conditional>
		
		<param type="integer" name="samtools_threads" value="8" min="1" label="Samtools: mpileup threads" />
		
		<conditional name="extended_parameters">
			<param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings.">
				<option value="default">Default settings</option>
				<option value="extended">Extended settings</option>
			</param>
			<when value="default">
			</when>
			<when value="extended">
				<param type="boolean" name="samtools_6" falsevalue="" truevalue=" -6" label="Samtools: assume the quality is in the Illumina-1.3+ encoding" />
				<param type="boolean" name="samtools_A" falsevalue="" truevalue=" -A" label="Samtools: count anomalous read pairs" />
				<param type="boolean" name="samtools_B" falsevalue="" truevalue=" -B" label="Samtools: disable BAQ computation" />
				<param type="integer" name="samtools_C" value="0"                     label="Samtools: parameter for adjusting mapQ; 0 to disable [0]" />
				<param type="integer" name="samtools_d" value="250"                   label="Samtools: max per-BAM depth to avoid excessive memory usage [250]" />
				<param type="boolean" name="samtools_E" falsevalue="" truevalue=" -E" label="Samtools: recalculate extended BAQ on the fly thus ignoring existing BQs" />
				<param type="integer" name="samtools_M" value="60"                    label="cap mapping quality at INT [60]" />
				<param type="boolean" name="samtools_R" falsevalue="" truevalue=" -R" label="Samtools: ignore RG tags" />
				<param type="integer" name="samtools_q" value="0"                     label="Samtools: skip alignments with mapQ smaller than INT [0]" />
				<param type="integer" name="samtools_Q" value="13"                    label="Samtools: skip bases with baseQ/BAQ smaller than INT [13]" />
				
				<param type="integer" name="samtools_e" value="20"                    label="Samtools: Phred-scaled gap extension seq error probability [20]" />
				<param type="float"   name="samtools_F" value="0.002"                 label="Samtools: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" />
				<param type="integer" name="samtools_h" value="100"                   label="Samtools: coefficient for homopolymer errors [100]" />
				<param type="boolean" name="samtools_I" falsevalue="" truevalue=" -I" label="Samtools: do not perform indel calling" />
				<param type="integer" name="samtools_L" value="250"                   label="Samtools: max per-sample depth for INDEL calling [250]" />
				<param type="integer" name="samtools_m" value="1"                     label="Samtools: minimum gapped reads for indel candidates [1]" help="Alias: -m" />
				<param type="integer" name="samtools_o" value="40"                    label="Samtools: Phred-scaled gap open sequencing error probability [40]" />
				<param type="boolean" name="samtools_p" falsevalue="" truevalue=" -p" label="Samtools: apply -m and -F per-sample to increase sensitivity" />
				<param type="text"    name="samtools_P" value="all"                   label="Samtools: comma separated list of platforms for indels [all]" />
				
				<param type="integer" name="varscan_min_coverage"     value="8"    label="VarScan: Minimum read depth at a position to make a call [8]" />
				<param type="integer" name="varscan_min_reads2"       value="2"    label="VarScan: PMinimum supporting reads at a position to call variants [2]" />
				<param type="integer" name="varscan_min_avg_qual"     value="15"   label="VarScan: Minimum base quality at a position to count a read [15]" />
				<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" />
				<param type="float"   name="varscan_min_freq_for_hom" value="0.75" label="VarScan: Minimum frequency to call homozygote [0.75]" />
				<param type="float"   name="varscan_p_value"          value="0.99" label="VarScan: Default p-value threshold for calling variants [99e-02]" />
				<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]" />
				<param type="boolean" name="varscan_variants"         falsevalue=" --variants 0"      truevalue=" --variants 1"                     label="VarScan: Report only variant (SNP/indel) positions [0]" />
			</when>
		</conditional>
		
		<param type="boolean" name="varscan_output_vcf" falsevalue=" --output-vcf 0" truevalue=" --output-vcf 1" label="VarScan: If set to 1, outputs in VCF format" />
	</inputs>
	
	<outputs>
		<data format="tabular" name="output_table" label="${tool.name}" />
	</outputs>
	
	<help>
		VarScan2.3.6
	</help>
</tool>