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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
author | erasmus-medical-center |
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date | Wed, 15 Feb 2017 16:16:01 -0500 |
parents | 0c5cc5763091 |
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<?xml version="1.0" encoding="UTF-8"?> <tool id="varscan_mpileup2snp_from_bam" name="VarScan2 Call SNPs from BAM" version="2.4.2.a"> <description>VarScan2 SNP/SNV detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.</description> <requirements> <requirement type="package" version="2.4.2">varscan</requirement> <requirement type="package" version="0.6.5">sambamba</requirement> </requirements> <version_command>varscan 2>&1 | head -n 1</version_command> <command detect_errors="exit_code"><![CDATA[ #for $alignment in $alignments ln -f -s '${alignment.metadata.bam_index}' '${alignment}.bai' && #end for sambamba mpileup -t \${GALAXY_SLOTS:-4} #for $alignment in $alignments '${alignment}' #end for --samtools -f #if $reference_genome_source.source_select == "indexed_filtered" '$reference_genome_source.reference_genome' #else if $reference_genome_source.source_select == "indexed_all" '$reference_genome_source.reference_genome' #else if $reference_genome_source.source_select == "history" '$reference_genome_source.reference_genome' #else <!-- This is a workaround to obtain the "genome.fa" file that corresponds to the dbkey of the alignments. Because this file is "calculated" during run-time, it can be used in a workflow. --> "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" #end if #if $extended_parameters_regions.sambamba_regions == "region" -r '${extended_parameters_regions.sambamba_r}' #elif $extended_parameters_regions.sambamba_regions == "regions_file_pos" or $extended_parameters_regions.sambamba_regions == "regions_file_bed" -l '${extended_parameters_regions.sambamba_l}' #end if #if $extended_parameters.parameters == "extended" $extended_parameters.sambamba_6 $extended_parameters.sambamba_A $extended_parameters.sambamba_B -C $extended_parameters.sambamba_C -d $extended_parameters.sambamba_d $extended_parameters.sambamba_E -M $extended_parameters.sambamba_M $extended_parameters.sambamba_R -q $extended_parameters.sambamba_q -Q $extended_parameters.sambamba_Q -e $extended_parameters.sambamba_e -F $extended_parameters.sambamba_F -h $extended_parameters.sambamba_h $extended_parameters.sambamba_I -L $extended_parameters.sambamba_L -m $extended_parameters.sambamba_m -o $extended_parameters.sambamba_o $extended_parameters.sambamba_p -P $extended_parameters.sambamba_P #end if | varscan mpileup2snp #if $extended_parameters.parameters == "extended" --min-coverage $extended_parameters.varscan_min_coverage --min-reads2 $extended_parameters.varscan_min_reads2 --min-avg-qual $extended_parameters.varscan_min_avg_qual --min-var-freq $extended_parameters.varscan_min_var_freq --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom --p-value $extended_parameters.varscan_p_value $extended_parameters.varscan_strand_filter $extended_parameters.varscan_variants #end if #if $varscan_output == "vcf" or $varscan_output.value == "vcf" --output-vcf 1 #end if > '$snv_output' ]]></command> <inputs> <param format="bam,sam" multiple="true" name="alignments" type="data" label="Alignment file(s)" help="Mapped reads in BAM or SAM format."/> <!-- Find out how to access the reference genome from the BAM file(s) --> <conditional name="reference_genome_source"> <param name="source_select" type="select" label="Fasta Source"> <option value="indexed_filtered">Use a built-in index (which fits your reference)</option> <option value="history">Use reference from the history</option> <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option> <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option> </param> <when value="history"> <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="indexed_filtered"> <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" > <options from_data_table="all_fasta"> <column name="name" index="2"/> <column name="dbkey" index="1"/> <column name="value" index="3"/><!-- Value is the path of the fasta file --> <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" /> <validator type="no_options" message="No indexes are available for the selected input dataset" /> </options> </param> </when> <when value="indexed_all"> <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" > <options from_data_table="all_fasta"> <column name="name" index="2"/> <column name="dbkey" index="1"/> <column name="value" index="3"/><!-- Value is the path of the fasta file --> <validator type="no_options" message="No indexes are available for the selected input dataset" /> </options> </param> </when> <when value="attribute" /> </conditional> <conditional name="extended_parameters_regions"> <param name="sambamba_regions" type="select" label="Region specific parameters" help="Let sambamba target specific genomic locations."> <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 value="region"> <param type="text" name="sambamba_r" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:pos or chr:start-end" /> </when> <when value="regions_file_pos"> <param type="data" name="sambamba_l" format="tabular" label="Samtools: list of positions (chr pos)" /> </when> <when value="regions_file_bed"> <param type="data" name="sambamba_l" format="bed" label="Samtools: specific regions (BED)" /> </when> </conditional> <conditional name="extended_parameters"> <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and sambamba settings."> <option value="default">Default settings</option> <option value="extended">Extended settings</option> </param> <when value="default" /> <when value="extended"> <param type="boolean" name="sambamba_6" falsevalue="" truevalue=" -6" label="Samtools: assume the quality is in the Illumina-1.3+ encoding" /> <param type="boolean" name="sambamba_A" falsevalue="" truevalue=" -A" label="Samtools: count anomalous read pairs" /> <param type="boolean" name="sambamba_B" falsevalue="" truevalue=" -B" label="Samtools: disable BAQ computation" /> <param type="integer" name="sambamba_C" value="0" label="Samtools: parameter for adjusting mapQ; 0 to disable [0]" /> <param type="integer" name="sambamba_d" value="250" label="Samtools: max per-BAM depth to avoid excessive memory usage [250]" /> <param type="boolean" name="sambamba_E" falsevalue="" truevalue=" -E" label="Samtools: recalculate extended BAQ on the fly thus ignoring existing BQs" /> <param type="integer" name="sambamba_M" value="60" label="cap mapping quality at INT [60]" /> <param type="boolean" name="sambamba_R" falsevalue="" truevalue=" -R" label="Samtools: ignore RG tags" /> <param type="integer" name="sambamba_q" value="0" label="Samtools: skip alignments with mapQ smaller than INT [0]" /> <param type="integer" name="sambamba_Q" value="13" label="Samtools: skip bases with baseQ/BAQ smaller than INT [13]" /> <param type="integer" name="sambamba_e" value="20" label="Samtools: Phred-scaled gap extension seq error probability [20]" /> <param type="float" name="sambamba_F" value="0.002" label="Samtools: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" /> <param type="integer" name="sambamba_h" value="100" label="Samtools: coefficient for homopolymer errors [100]" /> <param type="boolean" name="sambamba_I" falsevalue="" truevalue=" -I" label="Samtools: do not perform indel calling" /> <param type="integer" name="sambamba_L" value="250" label="Samtools: max per-sample depth for INDEL calling [250]" /> <param type="integer" name="sambamba_m" value="1" label="Samtools: minimum gapped reads for indel candidates [1]" help="Alias: -m" /> <param type="integer" name="sambamba_o" value="40" label="Samtools: Phred-scaled gap open sequencing error probability [40]" /> <param type="boolean" name="sambamba_p" falsevalue="" truevalue=" -p" label="Samtools: apply -m and -F per-sample to increase sensitivity" /> <param type="text" name="sambamba_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" checked="false" label="VarScan: Report only variant (SNP/indel) positions [0]" /> </when> </conditional> <param name="varscan_output" type="select" label="Output format"> <option value="vcf">VCF</option> <option value="tabular">tabular</option> </param> </inputs> <outputs> <data format="tabular" name="snv_output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}"> <change_format> <when input="varscan_output" value="vcf" format="vcf" /> </change_format> </data> </outputs> <tests> <test><!-- Use classical sambamba --> <param name="alignments" value="example.bam" ftype="bam" /> <param name="source_select" value="history" /> <param name="reference_genome" value="example.fa" /> <param name="sambamba_regions" value="entire_genome" /> <param name="parameters" value="default" /> <param name="varscan_output_vcf" value="1" /> <output name="snv_output" file="example.vcf" /> </test> </tests> <help> **VarScan 2.4.2** 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. http://dx.doi.org/10.1101/gr.129684.111 http://www.ncbi.nlm.nih.gov/pubmed/19542151 *VarScan* requires mpileup input files, generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing can be by-passed using this tool. Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan. .. _VarScan: http://varscan.sourceforge.net/ **Input formats** VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files must have a reference genome (dbkey) in Galaxy. Contact ------- The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) </help> <citations> <citation type="doi">10.1101/gr.129684.111</citation> </citations> </tool>