Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 90:8544e51f79bb draft
Deleted selected files
| author | yhoogstrate |
|---|---|
| date | Thu, 05 Nov 2015 08:29:18 -0500 |
| parents | a92c2ae342c4 |
| children | 94fb905e8d4f |
| files | samtools-parallel-mpileup.xml |
| diffstat | 1 files changed, 0 insertions(+), 300 deletions(-) [+] |
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--- a/samtools-parallel-mpileup.xml Thu Nov 05 08:21:31 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,300 +0,0 @@ -<?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="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 2>&1 | grep Version</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 -k1,1V -k2,2g - #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="example.bam" ftype="bam" /> - - <param name="source_select" value="history" /> - <param name="reference_genome" value="example.fa" ftypet="fasta" /> - - <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="example.mpileup" /> - </test> - <test><!-- Use parallelized samtools - @todo replace with sambamba! --> - <param name="alignments" value="example.bam" ftype="bam" /> - - <param name="source_select" value="history" /> - <param name="reference_genome" value="example.fa" ftypet="fasta" /> - - <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="example.mpileup.parallel" /> - </test> - </tests> - - <help> -**Samtools mpileup (supporting parallelization)** - -SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: - -Is flexible enough to store all the alignment information generated by various alignment programs; -Is simple enough to be easily generated by alignment programs or converted from existing alignment formats; -Is compact in file size; -Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory; -Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus. -SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. - -SAMtools is hosted by SourceForge.net. The project page is http://samtools.sourceforge.net/. The source code releases are available from the download page. You can check out the most recent source code from the github project page with: -git clone git://github.com/samtools/samtools.git -https://github.com/mydatascience/parallel-mpileup/ - -Because samtools does not support parallization of the mpileup command, the project was forked to include paralellization support: - - -However, since the project seems to lack support and contains fatal bugs this project was continued at: -https://github.com/yhoogstrate/parallel-mpileup/ - - -**Input formats** - -Satmools 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. - -**Installation** - -The installation is fully automatic. - -**License** - -* parallel-mpileup: MIT License (https://github.com/yhoogstrate/parallel-mpileup/blob/master/samtools-0.1.19/COPYING) -* samtool: MIT License - - -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.dtls.nl/ - -http://toolshed.g2.bx.psu.edu/ - -http://testtoolshed.g2.bx.psu.edu/ -</help> - <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