Mercurial > repos > yhoogstrate > varscan_mpileup2indel_from_bam
diff varscan_mpileup2indel.xml @ 1:2c56a59a112f draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122
| author | erasmus-medical-center |
|---|---|
| date | Wed, 15 Feb 2017 16:15:21 -0500 |
| parents | 10e2ea79ec55 |
| children |
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--- a/varscan_mpileup2indel.xml Thu Nov 05 10:00:19 2015 -0500 +++ b/varscan_mpileup2indel.xml Wed Feb 15 16:15:21 2017 -0500 @@ -1,41 +1,39 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="varscan_mpileup2indel" name="VarScan2 Call INDELs from a mpileup file" version="2.3.6.a"> - <description>VarScan2 INDEL detection; directly from a *.mpileup file.</description> +<tool id="varscan_mpileup2indel" name="VarScan2 Call INDELs from a mpileup file" version="2.4.2.a"> + <description>VarScan2 INDEL detection (on mpileup data)</description> <requirements> - <requirement type="package" version="2.3.6">varscan</requirement> + <requirement type="package" version="2.4.2">varscan</requirement> </requirements> - <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&1 | head -n 1</version_command> + <version_command>varscan 2>&1 | head -n 1</version_command> - <command> - cat $mpileup_input | java - -Xmx64G - -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar - mpileup2indel - - #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 - > $snv_output ; - cat stderr.txt - </command> + <command detect_errors="exit_code"><![CDATA[ + varscan mpileup2indel + + '${mpileup_input}' + + #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="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? --> + <param name="mpileup_input" format="pileup" type="data" label="Alignment file" + help="Mapped reads in mpileup format."/> <conditional name="extended_parameters"> <param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings."> @@ -45,12 +43,12 @@ <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="integer" name="varscan_min_coverage" value="8" label="Minimum read depth at a position to make a call [8]" /> + <param type="integer" name="varscan_min_reads2" value="2" label="Minimum supporting reads at a position to call variants [2]" /> + <param type="integer" name="varscan_min_avg_qual" value="15" label="Minimum base quality at a position to count a read [15]" /> + <param type="float" name="varscan_min_var_freq" value="0.01" label="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="Minimum frequency to call homozygote [0.75]" /> + <param type="float" name="varscan_p_value" value="0.99" label="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> @@ -81,51 +79,21 @@ </tests> <help> -**VarScan 2.3.6** +**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. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. http://dx.doi.org/10.1101/gr.129684.111 http://www.ncbi.nlm.nih.gov/pubmed/19542151 -*VarScan* requires mpileup formatted input files, which are generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing it is bypassed. Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan. -The samtools package is not able to parallelize the mpileup generation which make it a very slow process. -Other people were aware of this and have written a version that can do parallelization: -https://github.com/mydatascience/parallel-mpileup - -Consequently, when a BAM files gets processed by this wrapper, it's processed by *parallel-mpileup* before its send 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 have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing. +Alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing. **Installation** 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. - -**License** - -* VarScan2.3.6: Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0) -* parallel-mpileup: MIT License (https://github.com/mydatascience/parallel-mpileup/blob/master/samtools-0.1.19/COPYING) - -Contact -------- - -The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - -http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch - -More tools by the Translational Research IT (TraIT) project can be found -in the following toolsheds: - -http://toolshed.g2.bx.psu.edu/ - -http://testtoolshed.g2.bx.psu.edu/ </help> <citations> <citation type="doi">10.1101/gr.129684.111</citation> </citations> -</tool> \ No newline at end of file +</tool>