Mercurial > repos > yhoogstrate > samtools_parallel_mpileup
diff samtools-parallel-mpileup.xml @ 0:460f0749aac5 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
| author | yhoogstrate |
|---|---|
| date | Thu, 05 Nov 2015 07:49:02 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools-parallel-mpileup.xml Thu Nov 05 07:49:02 2015 -0500 @@ -0,0 +1,298 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="samtools_parallel_mpileup" name="Samtools parallel mpileup" version="0.1.19-a.a"> + <description>Samtools mpileup (supporting parallelization)</description> + + <requirements> + <requirement type="package" version="0.1.19-a">samtools_parallel_mpileup</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + + <version_command>samtools-parallel-mpileup 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" 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">No (uses original build of samtools)</option> + <option value="true" selected="true">Yes (uses samtools-parallel-mpileup)</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 forked 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.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