Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 87:f7798cd80cf5 draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
| author | yhoogstrate |
|---|---|
| date | Thu, 05 Nov 2015 04:14:09 -0500 |
| parents | c1424388f08b |
| children | aaf98cdc5916 |
| files | samtools-parallel-mpileup.xml varscan_mpileup2snp.xml varscan_mpileup2snp_from_bam.xml |
| diffstat | 3 files changed, 597 insertions(+), 578 deletions(-) [+] |
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--- a/samtools-parallel-mpileup.xml Thu Nov 05 03:45:02 2015 -0500 +++ b/samtools-parallel-mpileup.xml Thu Nov 05 04:14:09 2015 -0500 @@ -1,218 +1,221 @@ <?xml version="1.0" encoding="UTF-8"?> <tool id="samtools_parallel_mpileup" name="Samtools parallel mpileup" version="0.1.19a.a"> - <description>Samtools mpileup (supporting parallelization)</description> - <requirements> - <requirement type="package" version="6.0">ncurses</requirement> - <requirement type="package" version="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement> - <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement> - </requirements> - <command> - #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1 - echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2 - #else - #if $mpileup_parallelization.mpileup_parallelization_select == "true" - samtools-parallel-mpileup mpileup - -t $mpileup_parallelization.samtools_threads - #else - samtools mpileup - #end if - -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.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 $alignment in $alignments - ${alignment} - #end for - - 2> stderr_1.txt - - #if $sort_mpileup - | sort -k 1,1 -k 2,2 - #end if - - > $output ; - cat stderr_1.txt - #end if - </command> - - <inputs> - <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) --> - <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="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="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_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="samtools_regions" type="select" label="Region specific parameters" help="Let samtools 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> - <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> - - <conditional name="mpileup_parallelization"> - <param name="mpileup_parallelization_select" type="select" label="Use parallelization for the mpileup generation (experimental)" help="Especially if larger numbers of bam/sam files are processed, or the file infrastructure is optimized for IO-paralellization, this feature might improve performance."> - <option value="false" >False - uses classical samtools</option> - <option value="true">True - uses (experimental) samtools mpileup-parallel</option> - </param> - <when value="false" /> - <when value="true"> - <param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" /> - </when> - </conditional> - - <param name="sort_mpileup" type="boolean" truevalue="true" falsevalue="false" label="Sort mpileup file" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." /> - - <conditional name="extended_parameters"> - <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings."> - <option value="default">Default settings</option> - <option value="extended">Extended settings</option> - </param> - <when value="default" /> - <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]" /> - </when> - </conditional> - </inputs> - - <outputs> - <data format="mpileup" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> - </outputs> - - <tests> - <test><!-- Use classical samtools --> - <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <param name="source_select" value="attribute" /> - <param name="samtools_regions" value="entire_genome" /> - - <param name="mpileup_parallelization_select" value="false" /> - <param name="sort_mpileup" value="true" /> - - <param name="parameters" value="default" /> - - - <output name="output" file="hg19_mutant.mpileup" /> - </test> - <test><!-- Use parallelized samtools --> - <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <param name="source_select" value="attribute" /> - <param name="samtools_regions" value="entire_genome" /> - - <param name="mpileup_parallelization_select" value="true" /> - <param name="samtools_threads" value="2" /> - <param name="sort_mpileup" value="true" /> - - <param name="parameters" value="default" /> - - - <output name="output" file="hg19_mutant.mpileup" /> - </test> - </tests> - + <description>Samtools mpileup (supporting parallelization)</description> + + <requirements> + <requirement type="package" version="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement> + <requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement> + </requirements> + + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + + <command> + #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1 + echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2 + #else + #if $mpileup_parallelization.mpileup_parallelization_select == "true" + samtools-parallel-mpileup mpileup + -t $mpileup_parallelization.samtools_threads + #else + samtools mpileup + #end if + -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.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 $alignment in $alignments + ${alignment} + #end for + + 2> stderr_1.txt + + #if $sort_mpileup + | sort -k 1,1 -k 2,2 + #end if + + > $output ; + cat stderr_1.txt + #end if + </command> + + <inputs> + <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) --> + <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="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="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_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="samtools_regions" type="select" label="Region specific parameters" help="Let samtools 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> + <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> + + <conditional name="mpileup_parallelization"> + <param name="mpileup_parallelization_select" type="select" label="Use parallelization for the mpileup generation (experimental)" help="Especially if larger numbers of bam/sam files are processed, or the file infrastructure is optimized for IO-paralellization, this feature might improve performance."> + <option value="false">False - uses classical samtools</option> + <option value="true">True - uses (experimental) samtools mpileup-parallel</option> + </param> + <when value="false" /> + <when value="true"> + <param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" /> + </when> + </conditional> + + <param name="sort_mpileup" type="boolean" truevalue="true" falsevalue="false" label="Sort mpileup file" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." /> + + <conditional name="extended_parameters"> + <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings."> + <option value="default">Default settings</option> + <option value="extended">Extended settings</option> + </param> + <when value="default" /> + <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]" /> + </when> + </conditional> + </inputs> + + <outputs> + <data format="mpileup" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> + </outputs> + + <tests> + <test><!-- Use classical samtools --> + <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> + <param name="source_select" value="attribute" /> + <param name="samtools_regions" value="entire_genome" /> + + <param name="mpileup_parallelization_select" value="false" /> + <param name="sort_mpileup" value="true" /> + + <param name="parameters" value="default" /> + + + <output name="output" file="hg19_mutant.mpileup" /> + </test> + <test><!-- Use parallelized samtools --> + <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> + <param name="source_select" value="attribute" /> + <param name="samtools_regions" value="entire_genome" /> + + <param name="mpileup_parallelization_select" value="true" /> + <param name="samtools_threads" value="2" /> + <param name="sort_mpileup" value="true" /> + + <param name="parameters" value="default" /> + + + <output name="output" file="hg19_mutant.mpileup" /> + </test> + </tests> + <help> **Samtools mpileup (supporting parallelization)** @@ -268,12 +271,24 @@ http://testtoolshed.g2.bx.psu.edu/ </help> - <citation type="bibtex"> - @unpublished{samtools_parallel_mpileup, - author = {Youri Hoogstrate}, - title = { Samtools parallel-mpileup, fork of classical samtools }, - year = 2014, - url = { https://github.com/yhoogstrate/parallel-mpileup } - } - </citation> + <citations> + <citation type="bibtex"> + @unpublished{samtools_parallel_mpileup, + author = {Youri Hoogstrate}, + title = { Samtools parallel-mpileup, fork of classical samtools }, + year = 2014, + url = { https://github.com/yhoogstrate/parallel-mpileup } + } + </citation> + <citation type="bibtex"> + @misc{SAM_def, + title={Definition of SAM/BAM format}, + url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> </tool> \ No newline at end of file
--- a/varscan_mpileup2snp.xml Thu Nov 05 03:45:02 2015 -0500 +++ b/varscan_mpileup2snp.xml Thu Nov 05 04:14:09 2015 -0500 @@ -1,85 +1,86 @@ <?xml version="1.0" encoding="UTF-8"?> <tool id="varscan_mpileup2snp" name="VarScan2 Call SNPs from a mpileup file" version="2.3.6.a"> - <description>VarScan2 SNP/SNV detection; directly from a *.mpileup file.</description> - <requirements> - <requirement type="package" version="2.3.6">varscan</requirement> - </requirements> - - <version_command>java -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1</version_command> - - <command> - cat $mpileup_input | java - -Xmx64G - -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar - 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 - - 2> stderr.txt - > $snv_output ; - cat stderr.txt - </command> - - <inputs> - <param format="pileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/><!-- datatype "mpileup" does not exist.. it seems to be common to use pileup instead? --> - - <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="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 ${mpileup_input.hid}: ${mpileup_input.name}"> - <change_format> - <when input="varscan_output" value="vcf" format="vcf" /> - </change_format> - </data> - </outputs> - - <tests> - <test> - <param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="pileup" /> - <param name="parameters" value="default" /> - <param name="varscan_output_vcf" value="1" /> - - <output name="snv_output" file="hg19_mutant.vcf" /> - </test> - </tests> - - <help> + <description>VarScan2 SNP/SNV detection; directly from a *.mpileup file.</description> + + <requirements> + <requirement type="package" version="2.3.6">varscan</requirement> + </requirements> + + <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1</version_command> + + <command> + cat $mpileup_input | java + -Xmx64G + -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar + 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 + + 2> stderr.txt + > $snv_output ; + cat stderr.txt + </command> + + <inputs> + <param format="pileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in mpileup format."/><!-- datatype "mpileup" does not exist.. it seems to be common to use pileup instead? --> + + <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="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 ${mpileup_input.hid}: ${mpileup_input.name}"> + <change_format> + <when input="varscan_output" value="vcf" format="vcf" /> + </change_format> + </data> + </outputs> + + <tests> + <test> + <param name="mpileup_input" value="hg19_mutant.mpileup" dbkey="hg19" ftype="pileup" /> + <param name="parameters" value="default" /> + <param name="varscan_output_vcf" value="1" /> + + <output name="snv_output" file="hg19_mutant.vcf" /> + </test> + </tests> + + <help> **VarScan 2.3.6** 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.
--- a/varscan_mpileup2snp_from_bam.xml Thu Nov 05 03:45:02 2015 -0500 +++ b/varscan_mpileup2snp_from_bam.xml Thu Nov 05 04:14:09 2015 -0500 @@ -1,282 +1,285 @@ <?xml version="1.0" encoding="UTF-8"?> <tool id="varscan_mpileup2snp_from_bam" name="VarScan2 Call SNPs from BAM" version="2.3.6.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="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> - <requirement type="package" version="2.3.6">varscan</requirement> - <requirement type="package" version="5.9">ncurses</requirement> - </requirements> - <command> - #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1 - echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2 - #else - #import os.path - #for $alignment in $alignments - <!-- @todo use the existence of $alignment.metadata.bam_index or $alignment.metadata['bam_index'] --> - #if not os.path.isfile(str($alignment)+".bai") - echo "- Indexing alignment file: $alignment.name " ; - samtools index $alignment 2>&1 ; - #else - echo "- Skiping indexing: $alignment.name " ; - #end if - #end for - - #if $mpileup_parallelization.mpileup_parallelization_select == "true" - samtools-parallel-mpileup mpileup - -t $mpileup_parallelization.samtools_threads - #else - samtools mpileup - #end if - -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.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 $alignment in $alignments - ${alignment} - #end for - 2>stderr_1.txt - - #if $mpileup_parallelization.mpileup_parallelization_select == "true" - #if $mpileup_parallelization.sort_mpileup - | sort -k 1,1 -k 2,2 - #end if - #end if - - ## Make for every MPILEUP file an - ## http://en.wikipedia.org/wiki/Named_pipe - - | java - -Xmx64G - -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar - 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 - - 2>stderr_2.txt - > $snv_output ; - - - echo "---------------[ mpileup generation ]---------------" ; - cat stderr_1.txt ; - echo "" ; - echo "---------------[ VarScan SNP detect ]---------------" ; - cat stderr_2.txt ; - echo "" ; - echo "----------------------------------------------------" ; - #end if - </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="samtools_regions" type="select" label="Region specific parameters" help="Let samtools 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="samtools_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="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> - - <conditional name="mpileup_parallelization"> - <param name="mpileup_parallelization_select" type="select" label="Use parallelization for the mpileup generation (experimental)" help="Especially if larger numbers of bam/sam files are processed, or the file infrastructure is optimized for IO-paralellization, this feature might improve performance."> - <option value="false" >False - uses classical samtools</option> - <option value="true">True - uses (experimental) samtools mpileup-parallel</option> - </param> - <when value="false" /> - <when value="true"> - <param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" /> - <param type="boolean" name="sort_mpileup" truevalue="true" falsevalue="false" label="Sort mpileup file (SLOW)" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." /> - </when> - </conditional> - - <conditional name="extended_parameters"> - <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings."> - <option value="default">Default settings</option> - <option value="extended">Extended settings</option> - </param> - <when value="default" /> - <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" 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 samtools --> - <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <param name="source_select" value="attribute" /> - <param name="samtools_regions" value="entire_genome" /> - - <param name="mpileup_parallelization_select" value="false" /> - <param name="sort_mpileup" value="true" /> - - <param name="parameters" value="default" /> - <param name="varscan_output_vcf" value="1" /> - - - <output name="snv_output" file="hg19_mutant.vcf" /> - </test> - <test><!-- Use parallelized samtools --> - <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> - <param name="source_select" value="attribute" /> - <param name="samtools_regions" value="entire_genome" /> - - <param name="mpileup_parallelization_select" value="true" /> - <param name="samtools_threads" value="2" /> - <param name="sort_mpileup" value="true" /> - - <param name="parameters" value="default" /> - <param name="varscan_output_vcf" value="1" /> - - - <output name="snv_output" file="hg19_mutant.vcf" /> - </test> - </tests> - - <help> + <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="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + <requirement type="package" version="2.3.6">varscan</requirement> + </requirements> + + <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1</version_command> + + <command> + #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1 + echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2 + #else + #import os.path + #for $alignment in $alignments + <!-- @todo use the existence of $alignment.metadata.bam_index or $alignment.metadata['bam_index'] --> + #if not os.path.isfile(str($alignment)+".bai") + echo "- Indexing alignment file: $alignment.name " ; + samtools index $alignment 2>&1 ; + #else + echo "- Skiping indexing: $alignment.name " ; + #end if + #end for + + #if $mpileup_parallelization.mpileup_parallelization_select == "true" + samtools-parallel-mpileup mpileup + -t $mpileup_parallelization.samtools_threads + #else + samtools mpileup + #end if + -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.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 $alignment in $alignments + ${alignment} + #end for + 2>stderr_1.txt + + #if $mpileup_parallelization.mpileup_parallelization_select == "true" + #if $mpileup_parallelization.sort_mpileup + | sort -k 1,1 -k 2,2 + #end if + #end if + + ## Make for every MPILEUP file an + ## http://en.wikipedia.org/wiki/Named_pipe + + | java + -Xmx64G + -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar + 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 + + 2>stderr_2.txt + > $snv_output ; + + + echo "---------------[ mpileup generation ]---------------" ; + cat stderr_1.txt ; + echo "" ; + echo "---------------[ VarScan SNP detect ]---------------" ; + cat stderr_2.txt ; + echo "" ; + echo "----------------------------------------------------" ; + #end if + </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="samtools_regions" type="select" label="Region specific parameters" help="Let samtools 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="samtools_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="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> + + <conditional name="mpileup_parallelization"> + <param name="mpileup_parallelization_select" type="select" label="Use parallelization for the mpileup generation (experimental)" help="Especially if larger numbers of bam/sam files are processed, or the file infrastructure is optimized for IO-paralellization, this feature might improve performance."> + <option value="false" >False - uses classical samtools</option> + <option value="true">True - uses (experimental) samtools mpileup-parallel</option> + </param> + <when value="false" /> + <when value="true"> + <param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" /> + <param type="boolean" name="sort_mpileup" truevalue="true" falsevalue="false" label="Sort mpileup file (SLOW)" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." /> + </when> + </conditional> + + <conditional name="extended_parameters"> + <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings."> + <option value="default">Default settings</option> + <option value="extended">Extended settings</option> + </param> + <when value="default" /> + <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" 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 samtools --> + <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> + <param name="source_select" value="attribute" /> + <param name="samtools_regions" value="entire_genome" /> + + <param name="mpileup_parallelization_select" value="false" /> + <param name="sort_mpileup" value="true" /> + + <param name="parameters" value="default" /> + <param name="varscan_output_vcf" value="1" /> + + + <output name="snv_output" file="hg19_mutant.vcf" /> + </test> + <test><!-- Use parallelized samtools --> + <param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" /> + <param name="source_select" value="attribute" /> + <param name="samtools_regions" value="entire_genome" /> + + <param name="mpileup_parallelization_select" value="true" /> + <param name="samtools_threads" value="2" /> + <param name="sort_mpileup" value="true" /> + + <param name="parameters" value="default" /> + <param name="varscan_output_vcf" value="1" /> + + + <output name="snv_output" file="hg19_mutant.vcf" /> + </test> + </tests> + + <help> **VarScan 2.3.6** 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.