Mercurial > repos > jjohnson > gmap
changeset 11:6adc485b6dc0 draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Tue, 31 Jul 2012 08:19:46 -0400 |
| parents | 93911bac43da |
| children | |
| files | README gmap.xml gmap_build.xml gsnap.xml iit_store.xml lib/galaxy/datatypes/gmap.py snpindex.xml tool-data/datatypes_conf.xml tool-data/gmap_indices.loc.sample tool_dependencies.xml |
| diffstat | 10 files changed, 21 insertions(+), 2414 deletions(-) [+] |
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--- a/README Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -GMAP applications and citation info are available from: http://research-pub.gene.com/gmap/ - - - Installation instructions are in the README file in the download, - and online: http://research-pub.gene.com/gmap/src/README - - These tools were consistent with gmap version: 2011-11-30 - - -GMAP and GSNAP use added datatypes: - - add datatype definition file: lib/galaxy/datatypes/gmap.py - - add the following import line to: lib/galaxy/datatypes/registry.py - import gmap # added for gmap tools - - add to datatypes_conf.xml - <!-- Start GMAP Datatypes --> - <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/> - <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/> - <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/> - <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/> - <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/> - <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/> - <datatype extension="tally.iit" type="galaxy.datatypes.gmap:TallyIntervalIndexTree" display_in_upload="True"/> - <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/> - <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/> - <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/> - <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/> - <datatype extension="gsnap_tally" type="galaxy.datatypes.gmap:TallyAnnotation" display_in_upload="True"/> - <datatype extension="gsnap" type="galaxy.datatypes.gmap:GsnapResult" display_in_upload="True"/> - <!-- End GMAP Datatypes --> - -Tools: - GMAP_Build - create a GmapDB set of index files for a reference sequence and optional set of annotations - GMAP - map sequences to a reference sequence GmapDB index - GSNAP - align sequences to a reference and detect splicing - - Add to tool_conf.xml ( probably in the "NGS: Mapping" section ) - <tool file="gmap/gmap.xml" /> - <tool file="gmap/gsnap.xml" /> - <tool file="gmap/gmap_build.xml" /> - <tool file="gmap/snpindex.xml" /> - <tool file="gmap/iit_store.xml" /> - -Admin built cached gmapdb indexes defined in tool-data/gmap_indices.loc - - -TODO: - - - Add classes to gmap.py - CmetIndex - an index created by cmetindex - AtoiIndex - an index created by atoiindex - - Add tally creation - gsnap default output -> gsnap_tally -> iit_store - - Add goby support - Should add separate tools and datatypes for goby - GSNAP goby output relies on goby input, might be better to have a separate gsnap tool for goby - - Possibly add Tools: - get_genome - retrieves from a gmapdb - cmetindex - create methylcytosine index - atoiindex - create A-to-I RNA editing index - - - - -
--- a/gmap.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,482 +0,0 @@ -<tool id="gmap" name="GMAP" version="2.0.1"> - <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description> - <requirements> - <requirement type="binary">gmap</requirement> - </requirements> - <version_string>gmap --version</version_string> - <command> - #import os,os.path - gmap - --nthreads=4 --ordered - #if $refGenomeSource.genomeSource == "history": - --gseg=$refGenomeSource.ownFile - #elif $refGenomeSource.genomeSource == "gmapdb": - #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0] - --dir=$refGenomeSource.gmapdb.extra_files_path --db=$gmapdb - #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: - --kmer=$refGenomeSource.kmer - #end if - #else: - --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value) - #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: - --kmer=$refGenomeSource.kmer - #end if - #end if - #if $result.format == "summary": - --summary - #elif $result.format == "align": - --align - #elif $result.format == "continuous": - --continuous - #elif $result.format == "continuous-by-exon": - --continuous-by-exon - #elif $result.format == "compress": - --compress - #elif $result.format == "exons_dna": - --exons=cdna - #elif $result.format == "exons_gen": - --exons=genomic - #elif $result.format == "protein_dna": - --protein_dna - #elif $result.format == "protein_gen": - --protein_gen - #elif $result.format == "sam": - --format=$result.sam_paired_read - $result.no_sam_headers - #* Removed in gmap version 2011-11-30 - #if len($result.noncanonical_splices.__str__) > 0 - --noncanonical-splices=$result.noncanonical_splices - #end if - *# - #if len($result.read_group_id.__str__) > 0 - --read-group-id=$result.read_group_id - #end if - #if len($result.read_group_name.__str__) > 0 - --read-group-name=$result.read_group_name - #end if - #if len($result.read_group_library.__str__) > 0 - --read-group-library=$result.read_group_library - #end if - #if len($result.read_group_platform.__str__) > 0 - --read-group-platform=$result.read_group_platform - #end if - #elif $result.format != "gmap": - --format=$result.format - #end if - #if $computation.options == "advanced": - $computation.nosplicing - $computation.cross_species - #if len($computation.min_intronlength.__str__) > 0 - --min-intronlength=$computation.min_intronlength - #end if - #if len($computation.intronlength.__str__) > 0 - --intronlength=$computation.intronlength - #end if - #if len($computation.localsplicedist.__str__) > 0 - --localsplicedist=$computation.localsplicedist - #end if - #if len($computation.totallength.__str__) > 0 - --totallength=$computation.totallength - #end if - #if len($computation.trimendexons.__str__) > 0 - --trimendexons=$computation.trimendexons - #end if - --direction=$computation.direction - --canonical-mode=$computation.canonical - --prunelevel=$computation.prunelevel - --allow-close-indels=$computation.allow_close_indels - #if len($computation.microexon_spliceprob.__str__) >= 0: - --microexon-spliceprob=$computation.microexon_spliceprob - #end if - #if len($computation.chimera_margin.__str__) >= 0: - --chimera-margin=$computation.chimera_margin - #end if - #end if - #if $advanced.options == "used": - #if len($advanced.npaths.__str__) > 0: - --npaths=$advanced.npaths - #end if - #if len($advanced.suboptimal_score.__str__) > 0: - --suboptimal-score=$advanced.suboptimal_score - #end if - #if len($advanced.chimera_overlap.__str__) > 0: - --chimera_overlap=$advanced.chimera_overlap - #end if - $advanced.protein - $advanced.tolerant - $advanced.nolengths - $advanced.invertmode - #if len($advanced.introngap.__str__) > 0: - --introngap=$advanced.introngap - #end if - #if len($advanced.wraplength.__str__) > 0: - --wraplength=$advanced.wraplength - #end if - #end if - #if $split_output == True - $split_output - #end if - #if len($quality_protocol.__str__) > 0: - --quality-protocol=$quality_protocol - #end if - $input - #for $i in $inputs: - ${i.added_input} - #end for - #if $split_output == True - 2> $gmap_stderr - #else - 2> $gmap_stderr > $output - #end if - </command> - <inputs> - <!-- Input data --> - <param name="input" type="data" format="fasta,fastqsanger,fastqillumina" label="<H2>Input Sequences</H2>Select an mRNA or EST dataset to map" /> - <repeat name="inputs" title="addtional mRNA or EST dataset to map"> - <param name="added_input" type="data" format="fasta,fastqsanger,fastqillumina" label=""/> - </repeat> - <param name="quality_protocol" type="select" label="Protocol for input quality scores"> - <option value="">No quality scores</option> - <option value="sanger">Sanger quality scores</option> - <option value="illumina">Illumina quality scores</option> - </param> - - <!-- GMAPDB for mapping --> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="<HR><H2>Map To</H2>Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="gmapdb">Use gmapdb from the history</option> - <option value="history">Use a fasta reference sequence from the history</option> - </param> - <when value="indexed"> - <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="gmap_indices.loc"> - <column name="uid" index="0" /> - <column name="dbkey" index="1" /> - <column name="name" index="2" /> - <column name="kmers" index="3" /> - <column name="maps" index="4" /> - <column name="snps" index="5" /> - <column name="value" index="6" /> - </options> - </param> - <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size"> - <options from_file="gmap_indices.loc"> - <column name="name" index="3"/> - <column name="value" index="3"/> - <filter type="param_value" ref="gmapindex" column="6"/> - <filter type="multiple_splitter" column="3" separator=","/> - <filter type="add_value" name="" value=""/> - <filter type="sort_by" column="3"/> - </options> - </param> - <param name="map" type="select" data_ref="gmapindex" label="Look for splicing involving known sites or known introns" help=""> - <options from_file="gmap_indices.loc"> - <column name="name" index="4"/> - <column name="value" index="4"/> - <filter type="param_value" ref="gmapindex" column="6"/> - <filter type="multiple_splitter" column="4" separator=","/> - <filter type="add_value" name="" value=""/> - <filter type="sort_by" column="4"/> - </options> - </param> - </when> - <when value="gmapdb"> - <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" - help="A GMAP database built with GMAP Build"/> - <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size"> - <options> - <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/> - </options> - </param> - <param name="map" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help=""> - <options> - <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" - help="Fasta containing genomic DNA sequence"/> - </when> - </conditional> - - - <!-- Computation options --> - <conditional name="computation"> - <param name="options" type="select" label="<HR>Computational Settings" help=""> - <option value="default">Use default settings</option> - <option value="advanced">Set Computation Options</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/> - <param name="min_intronlength" type="integer" value="" optional="true" label="Min length for one internal intron (default 9)." help="Below this size, a genomic gap will be considered a deletion rather than an intron." > - <validator type="in_range" message="min_intronlength must be positive" min="0" /> - </param> - <param name="intronlength" type="integer" value="" optional="true" label="Max length for one intron (default 1000000)" > - <validator type="in_range" message="intronlength must be positive" min="0" /> - </param> - <param name="localsplicedist" type="integer" value="" optional="true" label="Max length for known splice sites at ends of sequence (default 200000)" > - <validator type="in_range" message="localsplicedist must be positive" min="0" /> - </param> - <param name="totallength" type="integer" value="" optional="true" label="Max total intron length (default 2400000)" > - <validator type="in_range" message="totallength must be positive" min="0" /> - </param> - <param name="chimera_margin" type="integer" value="" optional="true" label="Amount of unaligned sequence that triggers search for a chimera" - help=" default is 40, To turn off, set to a large value (greater than the query length)" > - <validator type="in_range" message="chimera_margin must be positive" min="0" /> - </param> - <param name="direction" type="select" label="cDNA direction"> - <option value="auto">auto</option> - <option value="sense_force">sense_force</option> - <option value="antisense_force">antisense_force</option> - <option value="sense_filter">sense_filter</option> - <option value="antisense_filter">antisense_filter</option> - </param> - <param name="trimendexons" type="integer" value="" optional="true" label="Trim end exons with fewer than given number of matches (in nt, default 12)" > - <validator type="in_range" message="trimendexons must be positive" min="1" /> - </param> - <param name="cross_species" type="boolean" truevalue="--cross-species" falsevalue="" checked="false" label="Cross-species alignment" help="For cross-species alignments, use a more sensitive search for canonical splicing"/> - - <param name="canonical" type="select" label="Reward for canonical and semi-canonical introns"> - <option value="1">high reward (default)</option> - <option value="0">low reward</option> - <option value="2">low reward for high-identity sequences</option> - </param> - <param name="allow_close_indels" type="select" label="Allow an insertion and deletion close to each other"> - <option value="1" selected="true">yes (default)</option> - <option value="0">no</option> - <option value="2">only for high-quality alignments</option> - </param> - <param name="microexon_spliceprob" type="float" value="" optional="true" label="Micro Exon splice probablility threshold" - help="Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90)" > - <validator type="in_range" message="slice probability between 0.00 and 1.00" min="0" max="1"/> - </param> - <param name="prunelevel" type="select" label="Pruning level"> - <option value="0">no pruning (default)</option> - <option value="1">poor sequences</option> - <option value="2">repetitive sequences</option> - <option value="3">poor and repetitive sequences</option> - </param> - <!-- could do this as a config file - <param name="chrsubsetfile" type="data" format="fasta" label="User-supplied chromosome subset file" /> - <param name="chrsubset" type="text" label="Chromosome subset to search" /> - --> - </when> - </conditional> - - <!-- Advanced Settings --> - <conditional name="advanced"> - <param name="options" type="select" label="<HR>Advanced Settings" help=""> - <option value="default">Use default settings</option> - <option value="used">Set Options</option> - </param> - <when value="default"/> - <when value="used"> - <param name="nolengths" type="boolean" checked="false" truevalue="--nolengths=true" falsevalue="" label="No intron lengths in alignment"/> - <param name="invertmode" type="select" label=" Mode for alignments to genomic (-) strand" help=""> - <option value="">Don't invert the cDNA (default)</option> - <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option> - <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option> - </param> - <param name="introngap" type="integer" value="" optional="true" label="Nucleotides to show on each end of intron (default=3)"> - <validator type="in_range" message="introngap must be positive" min="0" /> - </param> - <param name="wraplength" type="integer" value="" optional="true" label="Line Wrap length for alignment (default=50)"> - <validator type="in_range" message="wraplength must be positive" min="1" /> - </param> - <param name="npaths" type="integer" value="" optional="true" - label="Maximum number of paths to show. Ignored if negative. If 0, prints two paths if chimera detected, else one." > - <validator type="in_range" message="npaths must be positive" min="0" /> - </param> - <param name="suboptimal_score" type="integer" value="" optional="true" - label="Report only paths whose score is within this value of the best path" - help="By default the program prints all paths found." > - <validator type="in_range" message="suboptimal_score must be positive" min="0" /> - </param> - <param name="chimera_overlap" type="integer" value="" optional="true" label="Overlap to show, if any, at chimera breakpoint (default 0)" > - <validator type="in_range" message="chimera_overlap must be positive" min="0" /> - </param> - <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue="" - label="Translates cDNA with corrections for frameshifts"/> - <param name="protein" type="select" label="Protein alignment" help=""> - <option value="">default</option> - <option value="--fulllength=true">Assume full-length protein, starting with Met</option> - <option value="--truncate=true">Truncate alignment around full-length protein, Met to Stop</option> - </param> - </when> - </conditional> - - <!-- Output data --> - <conditional name="result"> - <param name="format" type="select" label="<HR><H2>Output</H2>Select the output format" help=""> - <option value="gmap">GMAP default output</option> - <option value="summary">Summary of alignments</option> - <option value="align">Alignment</option> - <option value="continuous">Alignment in three continuous lines</option> - <option value="continuous-by-exon">Alignment in three lines per exon</option> - <option value="compress">Print output in compressed format</option> - <option value="exons_dna">Print exons cDNA</option> - <option value="exons_gen">Print exons genomic</option> - <option value="protein_dna">Print protein sequence (cDNA)</option> - <option value="protein_gen">Print protein sequence (genomic)</option> - <option value="psl">PSL (BLAT) format</option> - <option value="gff3_gene">GFF3 gene format</option> - <option value="gff3_match_cdna">GFF3 match cDNA format</option> - <option value="gff3_match_est">GFF3 match EST format</option> - <option value="splicesites">splicesites output (for GSNAP)</option> - <option value="introns">introns output (for GSNAP)</option> - <option value="map_exons">IIT FASTA exon map format</option> - <option value="map_genes">IIT FASTA map format</option> - <option value="coords">coords in table format</option> - <option value="sam" selected="true">SAM format</option> - </param> - <when value="gmap"> - </when> - <when value="summary"/> - <when value="align"> - </when> - <when value="continuous"> - </when> - <when value="continuous-by-exon"> - </when> - <when value="compress"/> - <when value="exons_dna"/> - <when value="exons_gen"/> - <when value="protein_dna"/> - <when value="protein_gen"/> - <when value="psl"/> - <when value="gff3_gene"/> - <when value="gff3_match_cdna"/> - <when value="gff3_match_est"/> - <when value="splicesites"/> - <when value="introns"/> - <when value="map_exons"/> - <when value="map_genes"/> - <when value="coords"/> - <when value="sam"> - <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/> - <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/> - <!-- Removed in gmap version 2011-11-30 - <param name="noncanonical_splices" type="select" label="Print non-canonical genomic gaps greater than 20 nt in CIGAR string as STRING."> - <option value="">Use default</option> - <option value="N">N</option> - <option value="D">D</option> - </param> - --> - <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/> - <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/> - <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/> - <param name="read_group_platform" type="text" value="" label="Value to put into read-group library platform (RG-PL) field"/> - </when> - </conditional> <!-- name="result" --> - - <param name="split_output" type="boolean" truevalue="--split-output=gmap_out" falsevalue="" checked="false" label="Separate outputs for nomapping, uniq, mult, and chimera" help="(chimera only when chimera-margin is selected)"/> - - - <!-- - map=iitfile Map file. If argument is '?' (with the quotes), this lists available map files. - mapexons Map each exon separately - mapboth Report hits from both strands of genome - flanking=INT Show flanking hits (default 0) - print-comment Show comment line for each hit - --> - - - </inputs> - <outputs> - <data format="txt" name="gmap_stderr" label="${tool.name} on ${on_string}: stderr"/> - <data format="txt" name="output" label="${tool.name} on ${on_string} ${result.format}" > - <filter>(split_output == False)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - <data format="txt" name="uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gmap_out.uniq"> - <filter>(split_output == True)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - <data format="txt" name="transloc" label="${tool.name} on ${on_string} transloc.${result.format}" from_work_dir="gmap_out.transloc"> - <filter>(split_output == True)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gmap_out.nomapping"> - <filter>(split_output == True)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - <data format="txt" name="mult" label="${tool.name} on ${on_string} mult.${result.format}" from_work_dir="gmap_out.mult"> - <filter>(split_output == True)</filter> - <change_format> - <when input="result['format']" value="gff3_gene" format="gff3"/> - <when input="result['format']" value="gff3_match_cdna" format="gff3"/> - <when input="result['format']" value="gff3_match_est" format="gff3"/> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="splicesites" format="gmap_splicesites"/> - <when input="result['format']" value="introns" format="gmap_introns"/> - <when input="result['format']" value="map_genes" format="gmap_annotation"/> - <when input="result['format']" value="map_exons" format="gmap_annotation"/> - </change_format> - </data> - </outputs> - <tests> - </tests> - - <help> - -**What it does** - -GMAP_ (Genomic Mapping and Alignment Program) The functionality provided by gmap allows a user to: (1) map and align a single cDNA interactively against a large genome in about a second, without the startup time of several minutes typically needed by existing mapping programs; (2) switch arbitrarily among different genomes, without the need for a preloaded server dedicated to each genome; (3) run the program on computers with as little as 128 MB of RAM (random access memory); (4) perform high-throughput batch processing of cDNAs by using memory mapping and multithreading when appropriate memory and hardware are available; (5) generate accurate gene models, even in the presence of substantial polymorphisms and sequence errors; (6) locate splice sites accurately without the use of probabilistic splice site models, allowing generalized use of the program across species; (7) detect statistically significant microexons and incorporate them into the alignment; and (8) handle mapping and alignment tasks on genomes having alternate assemblies, linkage groups or strains. It is developed by Thomas D. Wu of Genentech, Inc. - -Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310 - -.. _GMAP: http://research-pub.gene.com/gmap/ -.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859 - ------- - -**Know what you are doing** - -.. class:: warningmark - -You will want to read the README_ - -.. _README: http://research-pub.gene.com/gmap/src/README - - </help> -</tool> -
--- a/gmap_build.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,174 +0,0 @@ -<tool id="gmap_build" name="GMAP Build" version="2.0.0"> - <description>a database genome index for GMAP and GSNAP</description> - <requirements> - <requirement type="binary">gmap_build</requirement> - </requirements> - <version_string>gmap --version</version_string> - <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command> - <inputs> - <!-- Name for this gmapdb --> - <param name="refname" type="text" label="Name you want to give this gmap database" help=""> - <validator type="empty_field" message="A database name is required."/> - </param> - <!-- Input data --> - <repeat name="inputs" title="Reference Sequence" min="1"> - <param name="input" type="data" format="fasta" label="reference sequence fasta" /> - </repeat> - - <param name="kmer" type="select" multiple="true" force_select="true" label="kmer size" help=""> - <option value="12">12</option> - <option value="13">13</option> - <option value="14">14</option> - <option value="15" selected="true">15</option> - </param> - <param name="cmetindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create cmetindex to process reads from bisulfite-treated DNA"/> - <param name="atoiindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create atoiindex to process reads under RNA-editing tolerance"/> - <conditional name="splicesite"> - <param name="splice_source" type="select" label="Add splice and intron info from" > - <option value="none"></option> - <option value="refGeneTable">refGenes table from UCSC table browser</option> - <option value="gtf">GTF</option> - <option value="gff3">GFF3</option> - </param> - <when value="none"/> - <when value="refGeneTable"> - <param name="refGenes" type="data" format="tabular" optional="true" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" /> - <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" - help="Note that alignment tracks in UCSC sometimes have an extra column on the left."> - <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/> - </param> - - </when> - <when value="gtf"> - <param name="gtfGenes" type="data" format="gtf" optional="true" label="Genes as GTF" help="" /> - </when> - <when value="gff3"> - <param name="gff3Genes" type="data" format="gff3" optional="true" label="Genes in GFF3 format" help="" /> - </when> - </conditional> - <conditional name="dbsnp"> - <param name="snp_source" type="select" label="Add SNP info from" > - <option value="none"></option> - <option value="snpTable">UCSC SNP Table</option> - <option value="snpFile">GMAP SNP File</option> - </param> - <when value="none"/> - <when value="snpTable"> - <param name="snps" type="data" format="tabular" optional="true" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" /> - <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" /> - <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help=""> - <option value="1" selected="true">1 (High)</option> - <option value="2">2 (Medium)</option> - <option value="3">3 (All)</option> - </param> - </when> - <when value="snpFile"> - <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file" - help="Format (3 columns): - <br>>rs62211261 21:14379270 CG - <br>>rs62211262 21:14379281 CG - <br>Each line must start with a > character, then be followed by an - identifier (which may have duplicates). Then there should be the - chromosomal coordinate of the SNP. (Coordinates are all 1-based, so - the first character of a chromosome is number 1.) Finally, there - should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN) - <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome. - If the one of these two letters does not match the allele in the reference - sequence, that SNP will be ignored in subsequent processing as a probable error. - The N stands for any other allele." /> - </when> - </conditional> - </inputs> - <outputs> - <!-- - <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> - --> - <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" /> - </outputs> - <configfiles> - <configfile name="shscript"> -#!/bin/bash -#set $ds = chr(36) -#set $gt = chr(62) -#set $lt = chr(60) -#set $ad = chr(38) -## #set $ref_files = '' -## #for $i in $inputs: - ## #set $ref_files = $ref_files $i.input -## #end for -## echo $ref_files -#import os.path -#set $gmapdb = $output.extra_files_path -#set $mapsdir = $os.path.join($os.path.join($gmapdb,str($refname)), str($refname) + '.maps') -mkdir -p $gmapdb -## export GMAPDB required for cmetindex and atoiindex -export GMAPDB=$gmapdb -#for $k in $kmer.__str__.split(','): -gmap_build -D $gmapdb -d $refname -s numeric-alpha -k $k #for i in $inputs# ${i.input}#end for# -#end for -get-genome -D $gmapdb -d '?' | sed 's/^Available .*/gmap db: /' -echo "kmers: " $kmer -#if $splicesite.splice_source == 'refGeneTable': -#if $splicesite.refGenes.__str__ != 'None': -cat $splicesite.refGenes | psl_splicesites -s $splicesite.col_skip | iit_store -o $os.path.join($mapsdir,'splicesites') -cat $splicesite.refGenes | psl_introns -s $splicesite.col_skip | iit_store -o $os.path.join($mapsdir,'introns') -#end if -#elif $splicesite.splice_source == 'gtf': -#if $splicesite.gtfGenes.__str__ != 'None': -cat $splicesite.gtfGenes | gtf_splicesites | iit_store -o $os.path.join($mapsdir,'splicesites') -cat $splicesite.gtfGenes | gtf_introns | iit_store -o $os.path.join($mapsdir,'introns') -#end if -#elif $splicesite.splice_source == 'gff3': -#if $splicesite.gff3Genes.__str__ != 'None': -cat $splicesite.gff3Genes | gff3_splicesites | iit_store -o $os.path.join($mapsdir,'splicesites') -cat $splicesite.gff3Genes | gff3_introns | iit_store -o $os.path.join($mapsdir,'introns') -#end if -#end if -#if $dbsnp.snp_source != 'none' and $dbsnp.snps.__str__ != 'None': -#if $dbsnp.snp_source == 'snpTable': -#if $dbsnp.snpsex.__str__ != 'None': -cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex | iit_store -o $os.path.join($mapsdir,'snps') -#else: -cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight | iit_store -o $os.path.join($mapsdir,'snps') -#end if -#else: -cat $dbsnp.snps | iit_store -o $os.path.join($mapsdir,'snps') -#end if -snpindex -d $refname -v snps -echo "snpindex" -d $refname -v snps -#end if -#if $cmetindex.__str__ == 'yes': -cmetindex -d $refname -echo "cmetindex" -d $refname -#end if -#if $atoiindex.__str__ == 'yes': -atoiindex -d $refname -echo "atoiindex" -d $refname -#end if -get-genome -D $gmapdb -d $refname -m '?' | sed 's/^Available maps .*/maps: /' - </configfile> - </configfiles> - - <tests> - </tests> - - <help> - - -**GMAP Build** - -GMAP Build creates an index of a genomic sequence for mapping and alignment using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). (GMAP Build uses GMSP commands: gmap_build, iit_store, psl_splicesites, psl_introns, gtf_splicesites, gtf_introns, gff3_splicesites, gff3_introns, dbsnp_iit, snpindex, cmetindex, and atoiindex.) - -You will want to read the README_ - -Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310 - -.. _GMAP: http://research-pub.gene.com/gmap/ -.. _GSNAP: http://research-pub.gene.com/gmap/ -.. _README: http://research-pub.gene.com/gmap/src/README -.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859 - - - </help> -</tool> -
--- a/gsnap.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,864 +0,0 @@ -<tool id="gsnap" name="GSNAP" version="2.0.1"> - <description>Genomic Short-read Nucleotide Alignment Program</description> - <requirements> - <requirement type="binary">gsnap</requirement> - </requirements> - <version_string>gsnap --version</version_string> - <command> - #import os.path, re - gsnap - --nthreads="4" --ordered - #if $refGenomeSource.genomeSource == "gmapdb": - #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0] - --dir=$refGenomeSource.gmapdb.extra_files_path --db=$refGenomeSource.gmapdb.metadata.db_name - #else: - --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value) - #end if - #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2: - --kmer=$refGenomeSource.kmer - #end if - #if $refGenomeSource.use_splicing.src == 'gmapdb': - #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: - -s $refGenomeSource.use_splicing.splicemap.value - #if $computation.trim_mismatch_score.__str__ == '0': - $ambig_splice_noclip - #end if - #end if - #elif $refGenomeSource.use_splicing.src == 'history': - #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: - -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap) - #if $computation.trim_mismatch_score.__str__ == '0': - $ambig_splice_noclip - #end if - #end if - #end if - #if $refGenomeSource.use_snps.src == 'gmapdb': - #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0: - -v $refGenomeSource.use_snps.snpindex.value - #end if - #elif $refGenomeSource.use_snps.src == 'history': - #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0: - -V $refGenomeSource.use_snps.snpindex.extra_files_path -v $refGenomeSource.use_snps.snpindex.metadata.snps_name - #end if - #end if - #if $refGenomeSource.mode.__str__ != '': - --mode=$refGenomeSource.mode - #end if - #* ## No longer in options as of version 2011-11-30 - #if $mapq_unique_score.__str__ != '': - --mapq-unique-score=$mapq_unique_score - #end if - *# - #if $computation.options == "advanced": - #if $computation.max_mismatches.__str__ != '': - --max-mismatches=$computation.max_mismatches - #end if - $computation.query_unk_mismatch - $computation.genome_unk_mismatch - #if $computation.terminal_threshold.__str__ != '': - --terminal-threshold=$computation.terminal_threshold - #end if - #if $computation.indel_penalty.__str__ != '': - --indel-penalty=$computation.indel_penalty - #end if - #if $computation.indel_endlength.__str__ != '': - --indel-endlength=$computation.indel_endlength - #end if - #if $computation.max_middle_insertions.__str__ != '': - --max-middle-insertions=$computation.max_middle_insertions - #end if - #if $computation.max_middle_deletions.__str__ != '': - --max-middle-deletions=$computation.max_middle_deletions - #end if - #if $computation.max_end_insertions.__str__ != '': - --max-end-insertions=$computation.max_end_insertions - #end if - #if $computation.max_end_deletions.__str__ != '': - --max-end-deletions=$computation.max_end_deletions - #end if - #if $computation.suboptimal_levels.__str__ != '': - --suboptimal-levels=$computation.suboptimal_levels - #end if - #if $computation.adapter_strip.__str__ != '': - --adapter-strip=$computation.adapter_strip - #end if - #if $computation.trim_mismatch_score.__str__ != '': - --trim-mismatch-score=$computation.trim_mismatch_score - #end if - #if $computation.trim_indel_score.__str__ != '': - --trim-indel-score=$computation.trim_indel_score - #end if - ## TODO - do we need these options (Is it tally XOR runlength?): - ## --tallydir= --use-tally=tally - ## --runlengthdir --use-runlength=runlength - #if $computation.use_tally != None and len($computation.use_tally.__str__) > 0: - ##--tallydir $os.path.dirname($computation.use_tally) --use-tally $os.path.basename($computation.use_tally) - --use-tally=$computation.use_tally - #end if - ## gmap options - #if $computation.gmap_mode.__str__ != '' and $computation.gmap_mode.__str__ != 'None': - --gmap-mode='$computation.gmap_mode' - #end if - #if $computation.trigger_score_for_gmap.__str__ != '': - --trigger-score-for-gmap=$computation.trigger_score_for_gmap - #end if - #if $computation.max_gmap_pairsearch.__str__ != '' and $re.search("pairsearch",$computation.gmap_mode): - --max-gmap-pairsearch=$computation.max_gmap_pairsearch - #end if - #if $computation.max_gmap_terminal.__str__ != '' and $re.search("terminal",$computation.gmap_mode): - --max-gmap-terminal=$computation.max_gmap_terminal - #end if - #if $computation.max_gmap_improvement.__str__ != '' and $re.search("improv",$computation.gmap_mode): - --max-gmap-improvement=$computation.max_gmap_improvement - #end if - #if $computation.microexon_spliceprob.__str__ != '': - --microexon-spliceprob=$computation.microexon_spliceprob - #end if - #end if - #if $splicing.options == "advanced": - $splicing.novelsplicing - #if $splicing.localsplicedist.__str__ != '': - --localsplicedist=$splicing.localsplicedist - #end if - #if $splicing.local_splice_penalty.__str__ != '': - --local-splice-penalty=$splicing.local_splice_penalty - #end if - #if $splicing.distant_splice_penalty.__str__ != '': - --distant-splice-penalty=$splicing.distant_splice_penalty - #end if - #if $splicing.local_splice_endlength.__str__ != '': - --local-splice-endlength=$splicing.local_splice_endlength - #end if - #if $splicing.distant_splice_endlength.__str__ != '': - --distant-splice-endlength=$splicing.distant_splice_endlength - #end if - #if $splicing.distant_splice_identity.__str__ != '': - --distant-splice-identity=$splicing.distant_splice_identity - #end if - #end if - #if $output.options == "advanced": - #if $output.npath.__str__ != '': - --npath=$output.npath - #end if - $output.quiet_if_excessive - $output.show_refdiff - $output.clip_overlap - #end if - #if $result.format == "sam": - --format=sam - $result.no_sam_headers - #if $result.read_group_id.__str__.strip != '': - --read-group-id='$result.read_group_id' - #end if - #if $result.read_group_name.__str__ != '': - --read-group-name='$result.read_group_name' - #end if - #if $result.read_group_library.__str__ != '': - --read-group-library='$result.read_group_library' - #end if - #if $result.read_group_platform.__str__ != '': - --read-group-platform='$result.read_group_platform' - #end if - #if $result.quality_shift.__str__ != '': - --quality-shift=$result.quality_shift - #end if - #elif $result.format == "goby": - #if $result.goby_output.__str__ != '': - --goby-output='$result.goby_output' - #end if - #if $result.creads_window_start.__str__ != '': - --creads-window-start=$result.creads_window_start - #end if - #if $result.creads_window_end.__str__ != '': - --creads-window-end=$result.creads_window_end - #end if - $result.creads_complement - #end if - #if $results.split_output == 'yes': - --split-output=gsnap_out - #if $results.fails.choice == 'nofails': - --nofails - #elif $results.fails.choice == 'failsonly': - --failsonly - #end if - $results.fails_as_input - #else - #if $results.fails.choice == 'nofails': - --nofails - #elif $results.fails.choice == 'failsonly': - --failsonly - $results.fails.fails_as_input - #end if - #end if - #if $seq.format == "gsnap_fasta": - $seq.circularinput $seq.gsnap - #else if $seq.format == "fastq": - #if $seq.barcode_length.__str__ != '': - --barcode-length=$seq.barcode_length - #end if - #if $seq.fastq_id_start.__str__ != '': - --fastq-id-start=$seq.fastq_id_start - #end if - #if $seq.fastq_id_end.__str__ != '': - --fastq-id-end=$seq.fastq_id_end - #end if - #if $seq.filter_chastity.__str__ != 'off': - --filter-chastity=$seq.filter_chastity - #end if - #if $seq.paired.ispaired.__str__ == 'yes': - #if $seq.paired.pairmax_dna.__str__ != '': - --pairmax-dna=$seq.paired.pairmax_dna - #end if - #if $seq.paired.pairmax_rna.__str__ != '': - --pairmax-rna=$seq.paired.pairmax_rna - #end if - #if $seq.paired.pairexpect.__str__ != '': - --pairexpect=$seq.paired.pairexpect - #end if - #if $seq.paired.pairdev.__str__ != '': - --pairdev=$seq.paired.pairdev - #end if - $seq.fastq $seq.paired.fastq - #else - $seq.fastq - #end if - #end if - #if $results.split_output == 'yes': - 2> $gsnap_stderr - #else: - #if $results.fails.choice.__str__ == 'failsonly' and $results.fails.fails_as_input.__str__ != '': - 2> $gsnap_stderr > $gsnap_fq - #else - 2> $gsnap_stderr > $gsnap_out - #end if - #end if - - </command> - <inputs> - <!-- Input data --> - <conditional name="seq"> - <param name="format" type="select" label="<H2>Input Sequences</H2>Select the input format" help=""> - <option value="fastq">Fastq</option> - <!-- - <option value="goby">Goby compact-reads</option> - --> - <option value="gsnap_fasta">GNSAP fasta</option> - </param> - <when value="fastq"> - <param name="fastq" type="data" format="fastq" label="Select a fastq dataset" /> - <conditional name="paired"> - <param name="ispaired" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use Paired Reads?"/> - <when value="no"/> - <when value="yes"> - <param name="fastq" type="data" format="fastq" label="Select the paired reads reverse dataset" /> - <param name="orientation" type="select" label="Orientation of paired-end reads" help=""> - <option value="FR">fwd-rev, typical Illumina default</option> - <option value="RF">rev-fwd, for circularized inserts</option> - <option value="FF">fwd-fwd, same strand</option> - </param> - <param name="pairmax_dna" type="integer" value="" optional="true" label="Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000)." help="Used if no splice file is provided and novelsplicing is off."/> - <param name="pairmax_rna" type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used when novel splicing is specified or a splice file is provided. Should probably match the value for localsplicedist."/> - <param name="pairexpect" type="integer" value="" optional="true" label="Expected paired-end length" - help="Used for calling splices in medial part of paired-end reads (default 200)"/> - <param name="pairdev" type="integer" value="" optional="true" label="Allowable deviation from expected paired-end length" - help="Used for calling splices in medial part of paired-end reads (default 25)"/> - </when> - </conditional> - <param name="barcode_length" type="integer" value="" optional="true" label="Amount of barcode to remove from start of read (default 0)" /> - <param name="fastq_id_start" type="integer" value="" optional="true" label="Starting field of identifier in FASTQ header, whitespace-delimited, starting from 1" /> - <param name="fastq_id_end" type="integer" value="" optional="true" label="Ending field of identifier in FASTQ header, whitespace-delimited, starting from 1" - help="Examples: - <br>@HWUSI-EAS100R:6:73:941:1973#0/1 - <br> . start=1, end=1 (default) => identifier is HWUSI-EAS100R:6:73:941:1973#0/1 - <br>@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36 - <br> . start=1, end=1 => identifier is SRR001666.1 - <br> . start=2, end=2 => identifier is 071112_SLXA-EAS1_s_7:5:1:817:345 - <br> . start=1, end=2 => identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345" - /> - <param name="filter_chastity" type="select" label="Skip reads marked by the Illumina chastity program" - help="String after the accession having a 'Y' after the first colon, like this: - <br>@accession 1:Y:0:CTTGTA - <br>where the 'Y' signifies filtering by chastity. - <br> For 'either', a 'Y' on either end of a paired-end read will be filtered. - <br> For 'both', a 'Y' is required on both ends of a paired-end read (or on the only end of a single-end read)" - > - <option value="off">off - no filtering</option> - <option value="either">either - a 'Y' on either end of a paired-end read</option> - <option value="both">both - a 'Y' is required on both ends of a paired-end read or the only end of a single-end read</option> - </param> - </when> - <!-- - <when value="goby"> - </when> - --> - <when value="gsnap_fasta"> - <param name="gsnap" type="data" format="fasta" label="Select a single-end dataset" help="GSNAP fasta must have the sequence entirely on one line, a second line is interpreted as the paired-end sequence"/> - <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/> - </when> - - </conditional> - <!-- No longer in options as of version 2011-11-30 - <param name="mapq_unique_score" type="integer" value="" optional="true" label="MAPQ score threshold" - help="For multiple results, consider as a unique result if only one of the results has a MAPQ score equal or greater than this - (if not selected, then reports all multiple results, up to npaths)" /> - --> - - <!-- GMAPDB for alignment --> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="<HR><H2>Align To</H2>Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="gmapdb">Use a gmapdb from your history</option> - </param> - <when value="indexed"> - <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="gmap_indices.loc"> - <column name="uid" index="0" /> - <column name="dbkey" index="1" /> - <column name="name" index="2" /> - <column name="kmers" index="3" /> - <column name="maps" index="4" /> - <column name="snps" index="5" /> - <column name="value" index="6" /> - </options> - </param> - - <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size"> - <options from_file="gmap_indices.loc"> - <column name="name" index="3"/> - <column name="value" index="3"/> - <filter type="param_value" ref="gmapindex" column="6"/> - <filter type="multiple_splitter" column="3" separator=","/> - <filter type="add_value" name="" value=""/> - <filter type="sort_by" column="3"/> - </options> - </param> - - <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase."> - <option value="">standard</option> - <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> - <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> - <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option> - <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option> - </param> - - <conditional name="use_splicing"> - <param name="src" type="select" label="<HR>Known Splicesite and Introns" - help="Look for splicing involving known sites or known introns at short or long distances - See README instructions for the distinction between known sites and known introns"> - <option value="none" selected="true">None</option> - <option value="gmapdb">From the GMAP Database</option> - <option value="history">A Map in your history</option> - </param> - <when value="none"/> - <when value="history"> - <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map" - help="built with GMAP IIT"/> - </when> - <when value="gmapdb"> - <param name="splicemap" type="select" data_ref="gmapindex" label="Use map for splicing involving known sites or known introns" help=""> - <options from_file="gmap_indices.loc"> - <column name="name" index="4"/> - <column name="value" index="4"/> - <filter type="param_value" ref="gmapindex" column="6"/> - <filter type="multiple_splitter" column="4" separator=","/> - <filter type="add_value" name="" value=""/> - <filter type="sort_by" column="4"/> - </options> - </param> - </when> - </conditional> - - <conditional name="use_snps"> - <param name="src" type="select" label="<HR>Known SNPs" help="for SNP tolerant alignments"> - <option value="none" selected="true">None</option> - <option value="gmapdb">From the GMAP Database</option> - <option value="history">A SNP Index in your history</option> - </param> - <when value="none"/> - <when value="history"> - <param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex" - help="built with GMAP SNP Index"/> - </when> - <when value="gmapdb"> - <param name="snpindex" type="select" data_ref="gmapindex" label="Use database containing known SNPs" help=""> - <options from_file="gmap_indices.loc"> - <column name="name" index="5"/> - <column name="value" index="5"/> - <filter type="param_value" ref="gmapindex" column="6"/> - <filter type="multiple_splitter" column="5" separator=","/> - <filter type="add_value" name="" value=""/> - <filter type="sort_by" column="5"/> - </options> - </param> - </when> - </conditional> - - </when> - <when value="gmapdb"> - <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" - help="A GMAP database built with GMAP Build"/> - <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size"> - <options> - <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/> - </options> - </param> - - <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase."> - <option value="">standard</option> - <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> - <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option> - <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option> - <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option> - </param> - - <conditional name="use_splicing"> - <param name="src" type="select" label="<HR>Known Splicesite and Introns" - help="Look for splicing involving known sites or known introns at short or long distances - See README instructions for the distinction between known sites and known introns"> - <option value="none" selected="true">None</option> - <option value="gmapdb">From the GMAP Database</option> - <option value="history">A Map in your history</option> - </param> - <when value="none"/> - <when value="history"> - <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map" - help="built with GMAP IIT"/> - <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites" - help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron. - This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/> - </when> - <when value="gmapdb"> - <param name="splicemap" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help=""> - <options> - <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> - </options> - </param> - <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites" - help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron. - This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/> - </when> - </conditional> - - <conditional name="use_snps"> - <param name="src" type="select" label="<HR>Known SNPs" help="for SNP tolerant alignments"> - <option value="none" selected="true">None</option> - <option value="gmapdb">From the GMAP Database</option> - <option value="history">A SNP Index in your history</option> - </param> - <when value="none"/> - <when value="history"> - <param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex" - help="built with GMAP SNP Index"/> - </when> - <when value="gmapdb"> - <param name="snpindex" type="select" data_ref="gmapdb" label="Use database containing known SNPs" help=""> - <options> - <filter type="data_meta" ref="gmapdb" key="snps" multiple="True" separator=","/> - </options> - </param> - </when> - </conditional> - - </when> - </conditional> - - <!-- Computation options --> - <conditional name="computation"> - <param name="options" type="select" label="<HR>Computational Settings" help=""> - <option value="default">Use default settings</option> - <option value="advanced">Set Computation Options</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="max_mismatches" type="float" value="" optional="true" label="Maximum number of mismatches allowed (uses default when negative)" - help="Defaults to the ultrafast level of ((readlength+2)/12 - 2)). - If specified between 0.0 and 1.0, then treated as a fraction - of each read length. Otherwise, treated as an integral number - of mismatches (including indel and splicing penalties) - For RNA-Seq, you may need to increase this value slightly - to align reads extending past the ends of an exon."> - <validator type="in_range" message="The mismatches must >= 0." min="0."/> - </param> - <param name="query_unk_mismatch" type="boolean" checked="false" truevalue="--query-unk-mismatch=1" falsevalue="" label="Count unknown (N) characters in the query as a mismatch"/> - <param name="genome_unk_mismatch" type="boolean" checked="true" truevalue="" falsevalue="--genome-unk-mismatch=0" label="Count unknown (N) characters in the genome as a mismatch"/> - <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 2)" - help="(from one end of the read to the best possible position at the other end). For example, if this value is 2, then if GSNAP finds an exact or - 1-mismatch alignment, it will not try to find a terminal alignment. - Note that this default value may not be low enough if you want to - obtain terminal alignments for very short reads, although such reads - probably don't have enough specificity for terminal alignments anyway." /> - <param name="indel_penalty" type="integer" value="" optional="true" label="Penalty for an indel (default 2)" - help="Counts against mismatches allowed. To find indels, make indel-penalty less than or equal to max-mismatches. A value < 2 can lead to false positives at read ends" /> - <param name="indel_endlength" type="integer" value="" optional="true" label="Minimum length at end required for indel alignments (default 4)" /> - <param name="max_middle_insertions" type="integer" value="" optional="true" label="Maximum number of middle insertions allowed (default 9)" /> - <param name="max_middle_deletions" type="integer" value="" optional="true" label="Maximum number of middle deletions allowed (default 30)" /> - <param name="max_end_insertions" type="integer" value="" optional="true" label="Maximum number of end insertions allowed (default 3)" /> - <param name="max_end_deletions" type="integer" value="" optional="true" label="Maximum number of end deletions allowed (default 6)" /> - <param name="suboptimal_levels" type="integer" value="" optional="true" label="Report suboptimal hits beyond best hit (default 0)" - help="All hits with best score plus suboptimal-levels are reported" /> - <param name="adapter_strip" type="select" label="Method for removing adapters from reads" - help="paired removes adapters from paired-end reads if a concordant or paired alignment cannot be found from the original read"> - <option value="paired" selected="true">paired</option> - <option value="off">off</option> - </param> - <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)" - help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive mismatches at the ends of reads)"/> - <param name="trim_indel_score" type="integer" value="" optional="true" label="Score to use for indels when trimming at ends (default is -4)" - help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive indels at the ends of reads)"/> - <param name="use_tally" type="data" format="tally.iit" optional="true" metadata_name="dbkey" label="Select a tally IIT file to resolve concordant multiple results" - help="generated by gsnap_tally and iit_store"/> - - <!-- - tallydir=STRING Directory for tally IIT file to resolve concordant multiple results (default is - location of genome index files specified using -D and -d). Note: can - just give full path name to use-tally instead. - use-tally=STRING Use this tally IIT file to resolve concordant multiple results - runlengthdir=STRING Directory for runlength IIT file to resolve concordant multiple results (default is - location of genome index files specified using -D and -d). Note: can - just give full path name to use-runlength instead. - use-runlength=STRING Use this runlength IIT file to resolve concordant multiple results - --> - - <!-- Options for GMAP alignment within GSNAP --> - <param name="gmap_mode" type="select" multiple="true" optional="true" display="checkboxes" label="Cases to use GMAP for complex alignments containing multiple splices or indels" - help="Default: pairsearch,terminal,improve"> - <option value="pairsearch" selected="true">pairsearch</option> - <option value="terminal" selected="true">terminal</option> - <option value="improve" selected="true">improve</option> - </param> - <param name="trigger_score_for_gmap" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 5)" - help="Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5)" /> - <param name="max_gmap_pairsearch" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 3)" - help="Perform GMAP pairsearch on nearby genomic regions up to this many candidate ends (default 3)." /> - <param name="max_gmap_terminal" type="integer" value="" optional="true" label="GMAP terminal threshold (default 3)" - help="Perform GMAP terminal on nearby genomic regions up to this many candidate ends (default 3)." /> - <param name="max_gmap_improvement" type="integer" value="" optional="true" label="GMAP improvement threshold (default 3)" - help="Perform GMAP improvement on nearby genomic regions up to this many candidate ends (default 3)." /> - <param name="microexon_spliceprob" type="float" value="" optional="true" label="GMAP microexons threshold (default .90)" - help="Allow microexons only if one of the splice site probabilities is greater than this value." > - <validator type="in_range" message="The microexons probability must be between 0. and 1." min="0." max="1."/> - </param> - </when> - </conditional> - - <conditional name="splicing"> - <param name="options" type="select" label="<HR>Splicing options for RNA-Seq" help=""> - <option value="default">Use default settings</option> - <option value="advanced">Set Splicing Options</option> - </param> - <when value="default"/> - <when value="advanced"> - <!-- Splicing options for RNA-Seq --> - <!-- use-splicing This should be either a select list from the gmapdb maps or a data type using splicesdir and use-splicing --> - <!-- Neither novel splicing (-N) nor known splicing (-s) turned on => assume reads are DNA-Seq (genomic) --> - <param name="novelsplicing" type="boolean" checked="false" truevalue="--novelsplicing=1" falsevalue="" label="Look for novel splicing "/> - <param name="localsplicedist" type="integer" value="" optional="true" label="Definition of local novel splicing event (default 200000)"/> - <param name="local_splice_penalty" type="integer" value="" optional="true" label="Penalty for a local splice (default 0). Counts against mismatches allowed"/> - <param name="distant_splice_penalty" type="integer" value="" optional="true" label="Penalty for a distant splice (default 3). Counts against mismatches allowed" - help="A distant splice is one where the intron length exceeds the value of localsplicedist or is an - inversion, scramble, or translocation between two different chromosomes. Counts against mismatches allowed"/> - <param name="distant_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for distant spliced alignments" - help="(default 16, min is the kmer length)"/> - <param name="shortend_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for short-end spliced alignments" - help="(default 2, but unless known splice sites are provided, GSNAP may still need the end length to be the value of kmer size to find a given splice"/> - <param name="distant_splice_identity" type="float" value="" optional="true" label="Minimum identity at end required for distant spliced alignments (default 0.95)"/> - <param name="antistranded_penalty" type="integer" value="" optional="true" label="Penalty for antistranded splicing when using stranded RNA-Seq protocols" - help="A positive value, such as 1, expects antisense on the first read and sense on the second read. - Default is 0, which treats sense and antisense equally well"/> - </when> - </conditional> - - <!-- Output data --> - <conditional name="output"> - <param name="options" type="select" label="<HR><H2>Output</H2>Output options for RNA-Seq" help=""> - <option value="default">Use default settings</option> - <option value="advanced">Set Output Options</option> - </param> - <when value="default"/> - <when value="advanced"> - <param name="npath" type="integer" value="" optional="true" label="Maximum number of paths to print (default 100)"/> - <param name="quiet_if_excessive" type="boolean" checked="false" truevalue="--quiet-if-excessive" falsevalue="" label="Quiet if Excessive" - help="If more than maximum number of paths are found, then nothing is printed."/> - <param name="show_refdiff" type="boolean" checked="false" truevalue="--show-refdiff" falsevalue="" label="Show SNP-tolerant alignment" - help="For GSNAP output in SNP-tolerant alignment, shows all differences relative to the reference genome as lower case (otherwise, it shows all differences relative to both the reference and alternate genome)"/> - <param name="clip_overlap" type="boolean" checked="false" truevalue="--clip-overlap" falsevalue="" label="Clip Overlap" - help="For paired-end reads whose alignments overlap, clip the overlapping region."/> - </when> - </conditional> - <conditional name="result"> - <param name="format" type="select" label="Select the output format" help=""> - <option value="sam">SAM</option> - <!-- goby should only be an option if the input is in goby format - <option value="goby">Goby</option> - --> - <option value="gsnap">GSNAP default output</option> - </param> - <when value="gsnap"> - </when> - <when value="sam"> - <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/> - <param name="read_group_id" type="text" value="" optional="true" label="Value to put into read-group id (RG-ID) field"/> - <param name="read_group_name" type="text" value="" optional="true" label="Value to put into read-group name (RG-SM) field"/> - <param name="read_group_library" type="text" value="" optional="true" label="Value to put into read-group library (RG-LB) field"/> - <param name="read_group_platform" type="text" value="" optional="true" label="Value to put into read-group library platform (RG-PL) field"/> - <param name="quality_shift" type="integer" value="" optional="true" label="Shift FASTQ quality scores by this amount in SAM output (default -31)"/> - </when> - <!-- - <when value="goby"> - <param name="goby_output" type="text" value="" label="Basename for Goby output files"/> - <param name="creads_window_start" type="integer" value="" optional="true" label="Compact reads window start (default: 0=start of file)"/> - <param name="creads_window_end" type="integer" value="" optional="true" label="Compact reads window end (default: 0=end of file)"/> - <param name="creads_complement" type="boolean" truevalue="-\-creads-complement" falsevalue="" checked="false" label="Complement read sequences (without reversing)"/> - </when> - --> - </conditional> - <!-- TODO combine fails and split_output --> - - <conditional name="results"> - <param name="split_output" type="select" label="<HR>Split outputs" - help="Separate outputs for: nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult results"> - <option value="no">no</option> - <option value="yes">yes</option> - </param> - <when value="no"> - <conditional name="fails"> - <param name="choice" type="select" label="How to deal with fails" help=""> - <option value="default">default - include them in results</option> - <option value="nofails">nofails - exclude fails from results</option> - <option value="failsonly">failsonly - only output failing results</option> - </param> - <when value="default"/> - <when value="nofails"/> - <when value="failsonly"> - <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format" - help=""/> - </when> - </conditional> - </when> - <when value="yes"> - <conditional name="fails"> - <param name="choice" type="select" label="How to deal with fails" help=""> - <option value="default">default - include them in results</option> - <option value="nofails">nofails - exclude fails from results</option> - <option value="failsonly">failsonly - only output failing results</option> - </param> - <when value="default"/> - <when value="nofails"/> - <when value="failsonly"/> - </conditional> - <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format" - help=""/> - </when> - </conditional> - - </inputs> - <outputs> - <data format="txt" name="gsnap_stderr" label="${tool.name} on ${on_string}: gsnap.log"/> - - <data format="txt" name="gsnap_out" label="${tool.name} on ${on_string} ${result.format}" > - <filter>(results['split_output'] == 'no' and (results['fails']['choice'] != 'failsonly' or results['fails']['fails_as_input'] == False))</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - - <data format="fastq" name="gsnap_fq" label="${tool.name} on ${on_string} fails.fq" > - <filter>(results['split_output'] == 'no' and results['fails']['choice'] == 'failsonly' and results['fails']['fails_as_input'] == True)</filter> - </data> - - <!-- nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, concordant_mult --> - - <data format="txt" name="unpaired_mult" label="${tool.name} on ${on_string} unpaired_mult.${result.format}" from_work_dir="gsnap_out.unpaired_mult"> - <filter>(results['split_output'] == 'yes')</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="unpaired_uniq" label="${tool.name} on ${on_string} unpaired_uniq.${result.format}" from_work_dir="gsnap_out.unpaired_uniq"> - <filter>(results['split_output'] == 'yes')</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="unpaired_transloc" label="${tool.name} on ${on_string} unpaired_transloc.${result.format}" from_work_dir="gsnap_out.unpaired_transloc"> - <filter>(results['split_output'] == 'yes')</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="halfmapping_mult" label="${tool.name} on ${on_string} halfmapping_mult.${result.format}" from_work_dir="gsnap_out.halfmapping_mult"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="halfmapping_uniq" label="${tool.name} on ${on_string} halfmapping_uniq.${result.format}" from_work_dir="gsnap_out.halfmapping_uniq"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="halfmapping_transloc" label="${tool.name} on ${on_string} halfmapping_transloc.${result.format}" from_work_dir="gsnap_out.halfmapping_transloc"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="paired_mult" label="${tool.name} on ${on_string} paired_mult.${result.format}" from_work_dir="gsnap_out.paired_mult"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="paired_uniq" label="${tool.name} on ${on_string} paired_uniq.${result.format}" from_work_dir="gsnap_out.paired_uniq"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="paired_transloc" label="${tool.name} on ${on_string} paired_transloc.${result.format}" from_work_dir="gsnap_out.paired_transloc"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - - <data format="txt" name="concordant_mult" label="${tool.name} on ${on_string} concordant_mult.${result.format}" from_work_dir="gsnap_out.concordant_mult"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="concordant_uniq" label="${tool.name} on ${on_string} concordant_uniq.${result.format}" from_work_dir="gsnap_out.concordant_uniq"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - <data format="txt" name="concordant_transloc" label="${tool.name} on ${on_string} concordant_transloc.${result.format}" from_work_dir="gsnap_out.concordant_transloc"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - - <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gsnap_out.nomapping"> - <filter>(results['split_output'] == 'yes' and results['fails_as_input'] == False)</filter> - <change_format> - <when input="result['format']" value="sam" format="sam"/> - <when input="result['format']" value="gsnap" format="gsnap"/> - </change_format> - </data> - - <data format="fastq" name="nomapping_fq" label="${tool.name} on ${on_string} nomapping.fq" from_work_dir="gsnap_out.nomapping.fq"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == False)</filter> - </data> - - <data format="fastq" name="nomapping_1_fq" label="${tool.name} on ${on_string} nomapping.1.fq" from_work_dir="gsnap_out.nomapping.1.fq"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - </data> - - <data format="fastq" name="nomapping_2_fq" label="${tool.name} on ${on_string} nomapping.2.fq" from_work_dir="gsnap_out.nomapping.2.fq"> - <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter> - </data> - - <!-- Will problay need wrapper code to generate composite datatype for goby alignment - <data format="gobyalignment" name="goby_alignment" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.nomapping"> - <filter>result['format'] == 'goby'</filter> - </data> - --> - - </outputs> - <tests> - </tests> - - <help> - -**What it does** - -GSNAP_ (Genomic Short-read Nucleotide Alignment Program) is a short read aligner which can align both single- and paired-end reads as short as 14nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state. It is developed by Thomas D. Wu of Genentech, Inc. -Publication_ citation: Thomas D. Wu, Serban Nacu "Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010 Apr 1;26(7):873-81. Epub 2010 Feb 10. - -.. _GSNAP: http://research-pub.gene.com/gmap/ -.. _Publication: http://bioinformatics.oupjournals.org/cgi/content/full/26/7/873 -http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844994/?tool=pubmed - ------- - -**Know what you are doing** - -.. class:: warningmark - -You will want to read the README_ - -.. _README: http://research-pub.gene.com/gmap/src/README - ------- - -**Input formats** - -Input to GSNAP should be either in FASTQ or FASTA format. - -The FASTQ input may include quality scores, which will then be included in SAM -output, if that output format is selected. - -For FASTA format, you should include one line per read (or end of a -paired-end read). The same FASTA file can have a mixture of -single-end and paired-end reads of varying lengths, if desired. - -Single-end reads: - -Each FASTA entry should contain one short read per line, like this - ->Header information -AAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTA - -Each short read can have a different length. However, the entire read -needs to be on a single line, and may not wrap around multiple lines. -If it extends to a second line, GSNAP will think that the read is -paired-end. - - -Paired-end reads: - -Each FASTA entry should contain two short reads, one per line, like -this - ->Header information -AAAACATTCTCCTCCGCATAAGCCTAGTAGATTA -GGCGTAGGTAGAAGTAGAGGTTAAGGCGCGTCAG - -By default, the program assumes that the second end is in the reverse -complement direction compared with the first end. If they are in the -same direction, you may need to use the --circular-input (or -c) flag. - -( The Galaxy tool: "FASTA Width formatter" can be used to reformat fasta files to have single line sequences. ) - ------- - -**Output formats in GSNAP** - -SAM output format - -Default GSNAP format - See the README_ - - - - - </help> -</tool> -
--- a/iit_store.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,181 +0,0 @@ -<tool id="gmap_iit_store" name="GMAP IIT" version="2.0.0"> - <description>Create a map store for known genes or SNPs</description> - <requirements> - <requirement type="binary">iit_store</requirement> - </requirements> - <version_string>iit_store --version</version_string> - <command interpreter="command"> /bin/bash $shscript 2> $log </command> - <inputs> - <!-- Input data --> - <conditional name="map"> - <param name="type" type="select" label="Make map for" > - <option value="genes">Introns and Splice sites</option> - <option value="snps">SNPs</option> - <option value="gmap">GMAP Annotation</option> - </param> - <when value="genes"> - <conditional name="src"> - <param name="src_format" type="select" label="Add splice and intron info from" > - <option value="refGeneTable">refGenes table from UCSC table browser</option> - <option value="gtf">GTF</option> - <option value="gff3">GFF3</option> - </param> - <when value="refGeneTable"> - <param name="genes" type="data" format="tabular" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" /> - <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" - help="Note that alignment tracks in UCSC sometimes have an extra column on the left."> - <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/> - </param> - </when> - <when value="gtf"> - <param name="genes" type="data" format="gtf" label="Genes as GTF" help="" /> - </when> - <when value="gff3"> - <param name="genes" type="data" format="gff3" label="Genes in GFF3 format" help="" /> - </when> - </conditional> - <param name="maps" type="select" display="checkboxes" multiple="true" force_select="true" label="Add splice and intron info from" > - <option value="splicesites" selected="true">splicesites.iit</option> - <option value="introns" selected="false">introns.iit</option> - </param> - </when> - <when value="snps"> - <conditional name="src"> - <param name="src_format" type="select" label="Add SNP info from" > - <option value="snpTable">UCSC SNP Table</option> - <option value="snpFile">GMAP SNP File</option> - </param> - <when value="snpTable"> - <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" /> - <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" /> - <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help=""> - <option value="1" selected="true">1 (High)</option> - <option value="2">2 (Medium)</option> - <option value="3">3 (All)</option> - </param> - </when> - <when value="snpFile"> - <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file" - help="Format (3 columns):<B> - <br>>rs62211261 21:14379270 CG - <br>>rs62211262 21:14379281 CG - </B> - <br>Each line must start with a > character, then be followed by an - identifier (which may have duplicates). Then there should be the - chromosomal coordinate of the SNP. (Coordinates are all 1-based, so - the first character of a chromosome is number 1.) Finally, there - should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN) - <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome. - If the one of these two letters does not match the allele in the reference - sequence, that SNP will be ignored in subsequent processing as a probable error. - The N stands for any other allele." /> - </when> - </conditional> - </when> - <when value="gmap"> - <param name="annotation" type="data" format="gmap_annotation" label="GMAP mapfile" - help="Format (2 or columns): <B> - <br>>label coords optional_tag - <br>optional_annotation (which may be zero, one, or multiple lines) - </B> - <br>Each line must start with a > character, then be followed by an identifier (which may have duplicates). - <br>Then there should be the chromosomal coordinate range. (Coordinates are all 1-based, so the first character of a chromosome is number 1.) - <br>The coords should be of the form - <br> chr:position - <br> chr:startposition..endposition - <br>The term chr:position is equivalent to chr:position..position. - <br>If you want to indicate that the interval is on the minus strand or reverse direction, then endposition may be less than startposition. - " /> - </when> - </conditional> - </inputs> - <outputs> - <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> - <data format="splicesites.iit" name="splicesites_iit" label="${tool.name} on ${on_string} splicesites.iit"> - <filter>(map['type'] == 'genes' and 'splicesites' in map['maps'])</filter> - </data> - <data format="introns.iit" name="introns_iit" label="${tool.name} on ${on_string} introns.iit"> - <filter>(map['type'] == 'genes' and 'introns' in map['maps'])</filter> - </data> - <data format="snps.iit" name="snps_iit" label="${tool.name} on ${on_string} snps.iit"> - <filter>(map['type'] == 'snps')</filter> - </data> - <data format="iit" name="map_iit" label="${tool.name} on ${on_string} map.iit"> - <filter>(map['type'] == 'gmap')</filter> - </data> - </outputs> - <configfiles> - <configfile name="shscript"> -#!/bin/bash -#set $catcmd = 'gzcat -f' -#set $catcmd = 'cat' -#set $ds = chr(36) -#set $gt = chr(62) -#set $lt = chr(60) -#set $ad = chr(38) -#set $ep = chr(33) -#set $toerr = ''.join([$gt,$ad,'2']) -#import os.path -#if $map.type == 'genes': -if [ $ep -e $map.src.genes ]; then echo "$map.src.genes does not exist" $toerr; exit 1; fi -if [ $ep -s $map.src.genes ]; then echo "$map.src.genes is empty" $toerr; exit 2; fi - #if $map.src.src_format == 'refGeneTable': - #if 'splicesites' in [ $map.maps.__str__ ]: - $catcmd $map.src.genes | psl_splicesites -s $map.src.col_skip | iit_store -o $splicesites_iit - #end if - #if 'introns' in [ $map.maps.__str__ ]: - $catcmd $map.src.genes | psl_introns -s $map.src.col_skip | iit_store -o $introns_iit - #end if - #elif $map.src.src_format == 'gtf': - #if 'splicesites' in [ $map.maps.__str__ ]: - $catcmd $map.src.genes | gtf_splicesites | iit_store -o $splicesites_iit - #end if - #if 'introns' in [ $map.maps.__str__ ]: - $catcmd $map.src.genes | gtf_introns | iit_store -o $introns_iit - #end if - #elif $map.src.src_format == 'gff3': - #if 'splicesites' in [ $map.maps.__str__ ]: - $catcmd $map.src.genes | gff3_splicesites | iit_store -o $splicesites_iit - #end if - #if 'introns' in [ $map.maps.__str__ ]: - $catcmd $map.src.genes | gff3_introns | iit_store -o $introns_iit - #end if - #end if -#elif $map.type == 'snps': -if [ $ep -s $map.src.snps ]; then echo "$map.src.snps is empty" $toerr; exit 2; fi - #if $map.src.snpsex.__str__ != 'None': - $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight -e $map.src.snpsex | iit_store -o $snps_iit - #else: - $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight | iit_store -o $snps_iit - #end if -#else: - $catcmd $map.src.snps | iit_store -o $map_iit -#end if - </configfile> - </configfiles> - - <tests> - </tests> - - <help> - - -**iit_store** - -GMAP IIT creates an Interval Index Tree map of known splice sites, introns, or SNPs (it uses iit_store described in the GMAP documentation). The maps can be used in GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). Maps are typically used for known splice sites, introns, or SNPs. - -You will want to read the README_ - -Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310 - -.. _GMAP: http://research-pub.gene.com/gmap/ -.. _GSNAP: http://research-pub.gene.com/gmap/ -.. _README: http://research-pub.gene.com/gmap/src/README -.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859 - - -**inputs** - - </help> -</tool> -
--- a/lib/galaxy/datatypes/gmap.py Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,472 +0,0 @@ -""" -GMAP indexes -""" -import logging -import os,os.path,re -import galaxy.datatypes.data -from galaxy.datatypes.data import Text -from galaxy import util -from galaxy.datatypes.metadata import MetadataElement - -log = logging.getLogger(__name__) - -class GmapDB( Text ): - """ - A GMAP DB for indexes - """ - MetadataElement( name="db_name", desc="The db name for this index set", default='unknown', set_in_upload=True, readonly=True ) - MetadataElement( name="basesize", default="12", desc="The basesize for offsetscomp", visible=True, readonly=True ) - MetadataElement( name="kmers", default=[''], desc="The kmer sizes for indexes", visible=True, no_value=[''], readonly=True ) - MetadataElement( name="map_dir", desc="The maps directory", default='unknown', set_in_upload=True, readonly=True ) - MetadataElement( name="maps", default=[''], desc="The names of maps stored for this gmap gmapdb", visible=True, no_value=[''], readonly=True ) - MetadataElement( name="snps", default=[''], desc="The names of SNP indexes stored for this gmapdb", visible=True, no_value=[''], readonly=True ) - MetadataElement( name="cmet", default=False, desc="Has a cmet index", visible=True, readonly=True ) - MetadataElement( name="atoi", default=False, desc="Has a atoi index", visible=True, readonly=True ) - - file_ext = 'gmapdb' - is_binary = True - composite_type = 'auto_primary_file' - allow_datatype_change = False - - def generate_primary_file( self, dataset = None ): - """ - This is called only at upload to write the html file - cannot rename the datasets here - they come with the default unfortunately - """ - return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' - - def regenerate_primary_file(self,dataset): - """ - cannot do this until we are setting metadata - """ - bn = dataset.metadata.db_name - log.info( "GmapDB regenerate_primary_file %s" % (bn)) - rval = ['<html><head><title>GMAPDB %s</title></head><p/><H3>GMAPDB %s</H3><p/>cmet %s<br>atoi %s<H4>Maps:</H4><ul>' % (bn,bn,dataset.metadata.cmet,dataset.metadata.atoi)] - for i,name in enumerate(dataset.metadata.maps): - rval.append( '<li>%s' % name) - rval.append( '</ul></html>' ) - f = file(dataset.file_name,'w') - f.write("\n".join( rval )) - f.write('\n') - f.close() - - def set_peek( self, dataset, is_multi_byte=False ): - log.info( "GmapDB set_peek %s" % (dataset)) - if not dataset.dataset.purged: - dataset.peek = "GMAPDB index %s\n cmet %s\n atoi %s\n maps %s" % ( dataset.metadata.db_name,dataset.metadata.cmet,dataset.metadata.atoi,dataset.metadata.maps ) - dataset.blurb = "GMAPDB %s" % ( dataset.metadata.db_name ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def display_peek( self, dataset ): - try: - return dataset.peek - except: - return "GMAP index file" - - def sniff( self, filename ): - return False - def set_meta( self, dataset, overwrite = True, **kwd ): - """ - Expecting: - extra_files_path/<db_name>/db_name>.ref<basesize><kmer>3<index> - extra_files_path/db_name/db_name.ref1[2345]1[2345]3offsetscomp - extra_files_path/db_name/db_name.ref1[2345]1[2345]3positions - extra_files_path/db_name/db_name.ref1[2345]1[2345]3gammaptrs - index maps: - extra_files_path/db_name/db_name.maps/*.iit - """ - log.info( "GmapDB set_meta %s %s" % (dataset,dataset.extra_files_path)) - pat = '(.*)\.((ref)|(met)[atgc][atgc]|(a2i)[atgc][atgc])((\d\d)(\d\d))?3positions(\.(.+))?' - efp = dataset.extra_files_path - flist = os.listdir(efp) - for i,fname in enumerate(flist): - log.info( "GmapDB set_meta %s %s" % (i,fname)) - fpath = os.path.join(efp,fname) - if os.path.isdir(fpath): - ilist = os.listdir(fpath) - kmers = {'':'default'} # HACK '' empty key added so user has default choice when selecting kmer from metadata - for j,iname in enumerate(ilist): - log.info( "GmapDB set_meta file %s %s" % (j,iname)) - ipath = os.path.join(fpath,iname) - if os.path.isdir(ipath): # find maps - dataset.metadata.map_dir = iname - for mapfile in os.listdir(ipath): - mapname = mapfile.replace('.iit','') - log.info( "GmapDB set_meta map %s %s" % (mapname,mapfile)) - dataset.metadata.maps.append(mapname) - else: - m = re.match(pat,iname) - if m: - log.info( "GmapDB set_meta m %s %s " % (iname, m)) - assert len(m.groups()) == 10 - dataset.metadata.db_name = fname - if m.groups()[2] == 'ref': - if m.groups()[-1] != None: - dataset.metadata.snps.append(m.groups()[-1]) - else: - if m.groups()[-3] != None: - k = int(m.groups()[-3]) - kmers[k] = k - if m.groups()[-4] != None: - dataset.metadata.basesize = int( m.groups()[-4]) - elif m.groups()[3] == 'met': - dataset.metadata.cmet = True - elif m.groups()[4] == 'a2i': - dataset.metadata.atoi = True - dataset.metadata.kmers = kmers.keys() - -class GmapSnpIndex( Text ): - """ - A GMAP SNP index created by snpindex - """ - MetadataElement( name="db_name", desc="The db name for this index set", default='unknown', set_in_upload=True, readonly=True ) - MetadataElement( name="snps_name", default='snps', desc="The name of SNP index", visible=True, no_value='', readonly=True ) - - file_ext = 'gmapsnpindex' - is_binary = True - composite_type = 'auto_primary_file' - allow_datatype_change = False - - def generate_primary_file( self, dataset = None ): - """ - This is called only at upload to write the html file - cannot rename the datasets here - they come with the default unfortunately - """ - return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' - - def regenerate_primary_file(self,dataset): - """ - cannot do this until we are setting metadata - """ - bn = dataset.metadata.db_name - log.info( "GmapDB regenerate_primary_file %s" % (bn)) - rval = ['<html><head><title>GMAPDB %s</title></head><p/><H3>GMAPDB %s</H3><p/>cmet %s<br>atoi %s<H4>Maps:</H4><ul>' % (bn,bn,dataset.metadata.cmet,dataset.metadata.atoi)] - for i,name in enumerate(dataset.metadata.maps): - rval.append( '<li>%s' % name) - rval.append( '</ul></html>' ) - f = file(dataset.file_name,'w') - f.write("\n".join( rval )) - f.write('\n') - f.close() - def set_peek( self, dataset, is_multi_byte=False ): - log.info( "GmapSnpIndex set_peek %s" % (dataset)) - if not dataset.dataset.purged: - dataset.peek = "GMAP SNPindex %s on %s\n" % ( dataset.metadata.snps_name,dataset.metadata.db_name) - dataset.blurb = "GMAP SNPindex %s on %s\n" % ( dataset.metadata.snps_name,dataset.metadata.db_name) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def display_peek( self, dataset ): - try: - return dataset.peek - except: - return "GMAP SNP index" - - def sniff( self, filename ): - return False - def set_meta( self, dataset, overwrite = True, **kwd ): - """ - Expecting: - extra_files_path/snp_name.iit - extra_files_path/db_name/db_name.ref1[2345]1[2345]3offsetscomp.snp_name - extra_files_path/db_name/db_name.ref1[2345]1[2345]3positions.snp_name - extra_files_path/db_name/db_name.ref1[2345]1[2345]3gammaptrs.snp_name - """ - log.info( "GmapSnpIndex set_meta %s %s" % (dataset,dataset.extra_files_path)) - pat = '(.*)\.(ref((\d\d)(\d\d))?3positions)\.(.+)?' - efp = dataset.extra_files_path - flist = os.listdir(efp) - for i,fname in enumerate(flist): - m = re.match(pat,fname) - if m: - assert len(m.groups()) == 6 - dataset.metadata.db_name = m.groups()[0] - dataset.metadata.snps_name = m.groups()[-1] - - - - -class IntervalIndexTree( Text ): - """ - A GMAP Interval Index Tree Map - created by iit_store - (/path/to/map)/(mapname).iit - """ - file_ext = 'iit' - is_binary = True - -class SpliceSitesIntervalIndexTree( IntervalIndexTree ): - """ - A GMAP Interval Index Tree Map - created by iit_store - """ - file_ext = 'splicesites.iit' - -class IntronsIntervalIndexTree( IntervalIndexTree ): - """ - A GMAP Interval Index Tree Map - created by iit_store - """ - file_ext = 'introns.iit' - -class SNPsIntervalIndexTree( IntervalIndexTree ): - """ - A GMAP Interval Index Tree Map - created by iit_store - """ - file_ext = 'snps.iit' - -class TallyIntervalIndexTree( IntervalIndexTree ): - """ - A GMAP Interval Index Tree Map - created by iit_store - """ - file_ext = 'tally.iit' - -class IntervalAnnotation( Text ): - """ - Class describing a GMAP Interval format: - >label coords optional_tag - optional_annotation (which may be zero, one, or multiple lines) - The coords should be of the form: - chr:position - chr:startposition..endposition - """ - file_ext = 'gmap_annotation' - """Add metadata elements""" - MetadataElement( name="annotations", default=0, desc="Number of interval annotations", readonly=True, optional=True, visible=False, no_value=0 ) - - def set_meta( self, dataset, **kwd ): - """ - Set the number of annotations and the number of data lines in dataset. - """ - data_lines = 0 - annotations = 0 - for line in file( dataset.file_name ): - line = line.strip() - if line and line.startswith( '>' ): - annotations += 1 - data_lines +=1 - else: - data_lines += 1 - dataset.metadata.data_lines = data_lines - dataset.metadata.annotations = annotations - def set_peek( self, dataset, is_multi_byte=False ): - if not dataset.dataset.purged: - dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) - if dataset.metadata.annotations: - dataset.blurb = "%s annotations" % util.commaify( str( dataset.metadata.annotations ) ) - else: - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - - def sniff( self, filename ): - """ - Determines whether the file is a gmap annotation file - Format: - >label coords optional_tag - optional_annotation (which may be zero, one, or multiple lines) - For example, the label may be an EST accession, with the coords - representing its genomic position. Labels may be duplicated if - necessary. - The coords should be of the form - chr:position - chr:startposition..endposition - The term "chr:position" is equivalent to "chr:position..position". If - you want to indicate that the interval is on the minus strand or - reverse direction, then <endposition> may be less than <startposition>. - """ - try: - pat = '>(\S+)\s((\S+):(\d+)(\.\.(\d+))?(\s.(.+))?$' #>label chr:position[..endposition][ optional_tag] - fh = open( filename ) - count = 0 - while True and count < 10: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: #first non-empty line - if line.startswith( '>' ): - count += 1 - if re.match(pat,line) == None: # Failed to match - return False - finally: - fh.close() - return False - -class SpliceSiteAnnotation(IntervalAnnotation): - file_ext = 'gmap_splicesites' - """ - Example: - >NM_004448.ERBB2.exon1 17:35110090..35110091 donor 6678 - >NM_004448.ERBB2.exon2 17:35116768..35116769 acceptor 6678 - >NM_004448.ERBB2.exon2 17:35116920..35116921 donor 1179 - >NM_004448.ERBB2.exon3 17:35118099..35118100 acceptor 1179 - >NM_004449.ERG.exon1 21:38955452..38955451 donor 783 - >NM_004449.ERG.exon2 21:38878740..38878739 acceptor 783 - >NM_004449.ERG.exon2 21:38878638..38878637 donor 360 - >NM_004449.ERG.exon3 21:38869542..38869541 acceptor 360 - Each line must start with a ">" character, then be followed by an - identifier, which may have duplicates and can have any format, with - the gene name or exon number shown here only as a suggestion. Then - there should be the chromosomal coordinates which straddle the - exon-intron boundary, so one coordinate is on the exon and one is on - the intron. (Coordinates are all 1-based, so the first character of a - chromosome is number 1.) Finally, there should be the splice type: - "donor" or "acceptor". You may optionally store the intron distance - at the end. GSNAP can use this intron distance, if it is longer than - its value for --localsplicedist, to look for long introns at that - splice site. The same splice site may have different intron distances - in the database; GSNAP will use the longest intron distance reported - in searching for long introns. - """ - def sniff( self, filename ): # TODO - """ - Determines whether the file is a gmap splice site annotation file - """ - try: - pat = '>(\S+\.intron\d+)\s((\S+):(\d+)\.\.(\d+))\s(donor|acceptor)(\s(\d+))?$' #>label chr:position..position donor|acceptor[ intron_dist] - fh = open( filename ) - count = 0 - while True and count < 10: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: #first non-empty line - count += 1 - if re.match(pat,line) == None: # Failed to match - return False - finally: - fh.close() - return False - -class IntronAnnotation(IntervalAnnotation): - file_ext = 'gmap_introns' - """ - Example: - >NM_004448.ERBB2.intron1 17:35110090..35116769 - >NM_004448.ERBB2.intron2 17:35116920..35118100 - >NM_004449.ERG.intron1 21:38955452..38878739 - >NM_004449.ERG.intron2 21:38878638..38869541 - The coordinates are 1-based, and specify the exon coordinates - surrounding the intron, with the first coordinate being from the donor - exon and the second one being from the acceptor exon. - """ - def sniff( self, filename ): # TODO - """ - Determines whether the file is a gmap Intron annotation file - """ - try: - pat = '>(\S+\.intron\d+)\s((\S+):(\d+)\.\.(\d+)(\s(.)+)?$' #>label chr:position - fh = open( filename ) - count = 0 - while True and count < 10: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: #first non-empty line - count += 1 - if re.match(pat,line) == None: # Failed to match - return False - finally: - fh.close() - return False - -class SNPAnnotation(IntervalAnnotation): - file_ext = 'gmap_snps' - """ - Example: - >rs62211261 21:14379270 CG - >rs62211262 21:14379281 AT - >rs62211263 21:14379298 WN - Each line must start with a ">" character, then be followed by an - identifier (which may have duplicates). Then there should be the - chromosomal coordinate of the SNP. (Coordinates are all 1-based, so - the first character of a chromosome is number 1.) Finally, there - should be the two possible alleles. (Previous versions required that - these be in alphabetical order: "AC", "AG", "AT", "CG", "CT", or "GT", - but that is no longer a requirement.) These alleles must correspond - to the possible nucleotides on the plus strand of the genome. If the - one of these two letters does not match the allele in the reference - sequence, that SNP will be ignored in subsequent processing as a - probable error. - - GSNAP also supports the idea of a wildcard SNP. A wildcard SNP allows - all nucleotides to match at that position, not just a given reference - and alternate allele. It is essentially as if an "N" were recorded at - that genomic location, although the index files still keep track of - the reference allele. To indicate that a position has a wildcard SNP, - you can indicate the genotype as "WN", where "W" is the reference - allele. Another indication of a wildcard SNP is to provide two - separate lines at that position with the genotypes "WX" and "WY", - where "W" is the reference allele and "X" and "Y" are two different - alternate alleles. - """ - def sniff( self, filename ): - """ - Determines whether the file is a gmap SNP annotation file - """ - try: - pat = '>(\S+)\s((\S+):(\d+)\s([TACGW][TACGN])$' #>label chr:position ATCG - fh = open( filename ) - count = 0 - while True and count < 10: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: #first non-empty line - count += 1 - if re.match(pat,line) == None: # Failed to match - return False - finally: - fh.close() - return False - - -class TallyAnnotation(IntervalAnnotation): - file_ext = 'gsnap_tally' - """ - Output produced by gsnap_tally - Example: - >144 chr20:57268791..57268935 - G0 - A1(1@7|1Q-3) - A2(1@36,1@1|1Q2,1Q-8) - C2 0.889,0.912,0.889,0.889,0.933,0.912,0.912,0.889,0.889,0.889 -2.66,-2.89,-2.66,-2.66,-3.16,-2.89,-2.89,-2.66,-2.66,-2.66 - C1 T1 0.888,0.9,0.888,0.9,0.913,0.9,0.911,0.888,0.9,0.913 -2.66,-2.78,-2.66,-2.78,-2.91,-2.78,-2.89,-2.66,-2.78,-2.91 - """ - def sniff( self, filename ): # TODO - """ - Determines whether the file is a gmap splice site annotation file - """ - try: - pat = '^>(\d+)\s((\S+):(\d+)\.\.(\d+))$' #>total chr:position..position - pat2 = '^[GATCN]\d.*$' #BaseCountDeatails - fh = open( filename ) - count = 0 - while True and count < 10: - line = fh.readline() - if not line: - break #EOF - line = line.strip() - if line: #first non-empty line - count += 1 - if re.match(pat,line) == None and re.match(pat2,line) == None: # Failed to match - return False - finally: - fh.close() - return False - -class GsnapResult( Text ): - """ - The default output format for gsnap. Can be used as input for gsnap_tally. - """ - file_ext = 'gsnap' - -
--- a/snpindex.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,136 +0,0 @@ -<tool id="gmap_snpindex" name="GMAP SNP Index" version="2.0.0"> - <description>build index files for known SNPs</description> - <requirements> - <requirement type="binary">snpindex</requirement> - </requirements> - <version_string>snpindex --version</version_string> - <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command> - <inputs> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Will you map to a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="gmapdb">Use gmapdb from the history</option> - </param> - <when value="indexed"> - <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_file="gmap_indices.loc"> - <column name="uid" index="0" /> - <column name="dbkey" index="1" /> - <column name="name" index="2" /> - <column name="kmers" index="3" /> - <column name="maps" index="4" /> - <column name="snps" index="5" /> - <column name="value" index="6" /> - </options> - </param> - </when> - <when value="gmapdb"> - <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb" - help="A GMAP database built with GMAP Build"/> - </when> - </conditional> - <conditional name="dbsnp"> - <param name="snp_source" type="select" label="Add SNP info from" > - <option value="snpTable">UCSC SNP Table</option> - <option value="snpFile">GMAP SNP File</option> - <option value="snpIIT">"GMAP SNPs map from GMAP iit store</option> - </param> - <when value="snpTable"> - <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" /> - <param name="snpsex" type="data" format="tabular" optional="true" label="UCSC SNP Exceptions table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130Exceptions.txt.gz" /> - <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help=""> - <option value="1" selected="true">1 (High)</option> - <option value="2">2 (Medium)</option> - <option value="3">3 (All)</option> - </param> - </when> - <when value="snpFile"> - <param name="snps" type="data" format="gmap_snps" label="GMAP SNPs file" - help="Format (3 columns): - <br>>rs62211261 21:14379270 CG - <br>>rs62211262 21:14379281 CG - <br>Each line must start with a > character, then be followed by an - identifier (which may have duplicates). Then there should be the - chromosomal coordinate of the SNP. (Coordinates are all 1-based, so - the first character of a chromosome is number 1.) Finally, there - should be the two possible alleles: ( AC AG AT CG CT GT or AN CN GN TN) - <br>These alleles must correspond to the possible nucleotides on the plus strand of the genome. - If the one of these two letters does not match the allele in the reference - sequence, that SNP will be ignored in subsequent processing as a probable error. - The N stands for any other allele." /> - </when> - <when value="snpIIT"> - <param name="snpIIT" type="data" format="snps.iit" label="GMAP SNPs map" help="Created by: GMAP iit store" /> - </when> - </conditional> - <param name="snps_name" type="text" value="snps" label="Name for this SNP index" help="no white space characters"> - </param> - </inputs> - <outputs> - <!-- - <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/> - --> - <data format="gmapsnpindex" name="output" label="${tool.name} on ${on_string} snpindex" /> - </outputs> - <configfiles> - <configfile name="shscript"> -#!/bin/bash -#set $ds = chr(36) -#set $gt = chr(62) -#set $lt = chr(60) -#set $ad = chr(38) -#import os.path -#if $refGenomeSource.genomeSource == "gmapdb": -#set $gmapdb = $refGenomeSource.gmapdb.extra_files_path -#set $refname = $refGenomeSource.gmapdb.metadata.db_name -#else: -#set $gmapdb = $os.path.dirname($refGenomeSource.gmapindex.value) -$refname = $os.path.basename($refGenomeSource.gmapindex.value) -#end if -#set $gmapsnpdir = $output.extra_files_path -mkdir -p $gmapsnpdir -#set $snpsname = $snps_name.__str__ -#set $snpsiit = '.'.join([$snpsname,'iit']) -#set $pathsnps = $os.path.join($gmapsnpdir,$snpsname) -#set $pathsnpsiit = $os.path.join($gmapsnpdir,$snpsiit) -#if $dbsnp.snp_source != 'none' and $dbsnp.snps.__str__ != 'None': -#if $dbsnp.snp_source == 'snpTable': -#if $dbsnp.snpsex.__str__ != 'None': -cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex | iit_store -o $pathsnps -#else: -cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight | iit_store -o $pathsnps -#end if -#elif $dbsnp.snp_source == 'snpFile': -cat $dbsnp.snps | iit_store -o $pathsnps -#elif $dbsnp.snp_source == 'snpIIT': -cat $dbsnp.snps > $pathsnpsiit -#end if -snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit -echo snpindex -D $gmapdb -d $refname -V $output.extra_files_path -v $snpsname $pathsnpsiit -#end if - </configfile> - </configfiles> - - <tests> - </tests> - - <help> - - -**GMAP SNP Index** - -GMAP SNP Index (snpindex in the GMAP documentaion) creates an index for known SNPs allowing for SNP tolerant mapping and alignment when using GMAP_ (Genomic Mapping and Alignment Program for mRNA and EST sequences) and GSNAP_ (Genomic Short-read Nucleotide Alignment Program). - -You will want to read the README_ - -Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310 - -.. _GMAP: http://research-pub.gene.com/gmap/ -.. _GSNAP: http://research-pub.gene.com/gmap/ -.. _README: http://research-pub.gene.com/gmap/src/README -.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859 - - - </help> -</tool> -
--- a/tool-data/datatypes_conf.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -<?xml version="1.0"?> -<datatypes> - <datatype_files> - <datatype_file name="gmap.py"/> - </datatype_files> - <registration> - <datatype extension="gmapdb" type="galaxy.datatypes.gmap:GmapDB" display_in_upload="False"/> - <datatype extension="gmapsnpindex" type="galaxy.datatypes.gmap:GmapSnpIndex" display_in_upload="False"/> - <datatype extension="iit" type="galaxy.datatypes.gmap:IntervalIndexTree" display_in_upload="True"/> - <datatype extension="splicesites.iit" type="galaxy.datatypes.gmap:SpliceSitesIntervalIndexTree" display_in_upload="True"/> - <datatype extension="introns.iit" type="galaxy.datatypes.gmap:IntronsIntervalIndexTree" display_in_upload="True"/> - <datatype extension="snps.iit" type="galaxy.datatypes.gmap:SNPsIntervalIndexTree" display_in_upload="True"/> - <datatype extension="gmap_annotation" type="galaxy.datatypes.gmap:IntervalAnnotation" display_in_upload="False"/> - <datatype extension="gmap_splicesites" type="galaxy.datatypes.gmap:SpliceSiteAnnotation" display_in_upload="True"/> - <datatype extension="gmap_introns" type="galaxy.datatypes.gmap:IntronAnnotation" display_in_upload="True"/> - <datatype extension="gmap_snps" type="galaxy.datatypes.gmap:SNPAnnotation" display_in_upload="True"/> - </registration> - <sniffers> - <sniffer type="galaxy.datatypes.gmap:IntervalAnnotation"/> - <sniffer type="galaxy.datatypes.gmap:SpliceSiteAnnotation"/> - <sniffer type="galaxy.datatypes.gmap:IntronAnnotation"/> - <sniffer type="galaxy.datatypes.gmap:SNPAnnotation"/> - </sniffers> -</datatypes>
--- a/tool-data/gmap_indices.loc.sample Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of GMAPDB indexed sequences data files. You will need -#to create these data files using gmap_build and then create a gmap_indices.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The gmap_indices.loc -#file has this format (white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <kmers> <map,map> <snp,snp> <file_base_path> -#hg18 hg18 hg18 (cmet atoi) 12,13,14,15 splicesites,introns snps /depot/data2/galaxy/gmap/hg18 -#hg19 hg19 hg19 (cmet atoi) 12,13,14,15 splicesites,introns,snps snps,dbsnp /depot/data2/galaxy/gmap/hg19
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jul 31 08:19:46 2012 -0400 @@ -0,0 +1,21 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="gmap" version="0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8"> + <install version="1.0"> + <actions> + <action type="shell_command">wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2011-11-30.tar.gz</action> + <action type="shell_command"> ./configure --prefix=bin --with-gmapdb=../gmapdb</action> + <action type="shell_command">make</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + </readme> + </package> +</tool_dependency>