Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 12:50ab1eb510d8
Uploaded
author | yhoogstrate |
---|---|
date | Thu, 30 Jan 2014 07:49:08 -0500 |
parents | dd96b65174df |
children | 324717caecb8 |
files | varscan2_from_bam.xml |
diffstat | 1 files changed, 59 insertions(+), 35 deletions(-) [+] |
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--- a/varscan2_from_bam.xml Thu Dec 19 07:11:05 2013 -0500 +++ b/varscan2_from_bam.xml Thu Jan 30 07:49:08 2014 -0500 @@ -1,6 +1,6 @@ <?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> +<tool id="varscan2_snp_from_bam" name="VarScan2 from BAM"> + <description>VarScan2 SNP detection (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> @@ -8,7 +8,12 @@ <command> samtools-mpileup-parallel mpileup -t $samtools_threads - -f $reference_genome + -f + #if $reference_genome_source.source_select=="database" + $reference_genome_source.reference_genome + #else + $reference_genome_source.reference_genome + #end if #if $extended_parameters_regions.samtools_regions == "region" -r $extended_parameters_regions.$samtools_r @@ -39,8 +44,8 @@ -P $extended_parameters.samtools_P #end if - #for $sample in $samples - ${sample.mapped_reads} + #for $alignment in $alignments + ${alignment} #end for | java @@ -49,12 +54,12 @@ 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-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 + --p-value $varscan_p_value $varscan_strand_filter $varscan_output_vcf $varscan_variants @@ -66,12 +71,28 @@ </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> + <param format="bam,sam" multiple="true" name="alignments" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/> <!-- 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="reference_genome_source"> + <param name="source_select" type="select" label="Fasta Source"> + <option value="cached" selected="true">Locally Cached Alignments</option> + <option value="user">Alignments in Your History</option> + </param> + <when value="user"> + <param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (fasta)" help="Reference genome (genome.fa) that corresponds to the *.bam file." /> + </when> + <when value="cached"> + <param name="reference_genome" type="select" label="Reference Genome used during alignment (fasta)" > + <options from_file="all_fasta.loc"> + <column name="name" index="0"/> + <column name="dbkey" index="1"/> + <column name="value" index="3"/> + <filter type="data_meta" ref="alignments" multiple="true" key="dbkey" column="1" /> + </options> + </param> + </when> + </conditional> <conditional name="extended_parameters_regions"> <param name="samtools_regions" type="select" label="VarScan parameters" help="For more advanced VarScan settings."> @@ -89,7 +110,7 @@ <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)" /> + <param type="data" name="samtools_l" format="bed" label="Samtools: specific regions (BED)" /> </when> </conditional> @@ -106,32 +127,32 @@ <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="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="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_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="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="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="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="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]" /> + <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> @@ -139,10 +160,13 @@ </inputs> <outputs> - <data format="tabular" name="output_table" label="${tool.name}" /> + <data format="tabular" name="output_table" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> </outputs> <help> VarScan2.3.6 + ------------ + + Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment. </help> </tool>