view samtools-parallel-mpileup.xml @ 86:c1424388f08b draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty

<?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!" >&amp;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)**

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>
	<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>
</tool>