| Previous changeset 10:93911bac43da (2012-01-05) |
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Commit message:
Uploaded |
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added:
tool_dependencies.xml |
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removed:
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 |
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| diff -r 93911bac43da -r 6adc485b6dc0 README --- a/README Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 - - - - - |
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| diff -r 93911bac43da -r 6adc485b6dc0 gmap.xml --- a/gmap.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,482 +0,0 @@\n-<tool id="gmap" name="GMAP" version="2.0.1">\n- <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description>\n- <requirements>\n- <requirement type="binary">gmap</requirement>\n- </requirements>\n- <version_string>gmap --version</version_string>\n- <command>\n- #import os,os.path\n- gmap\n- --nthreads=4 --ordered\n- #if $refGenomeSource.genomeSource == "history":\n- --gseg=$refGenomeSource.ownFile\n- #elif $refGenomeSource.genomeSource == "gmapdb":\n- #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0]\n- --dir=$refGenomeSource.gmapdb.extra_files_path --db=$gmapdb\n- #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:\n- --kmer=$refGenomeSource.kmer\n- #end if\n- #else:\n- --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value)\n- #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:\n- --kmer=$refGenomeSource.kmer\n- #end if\n- #end if\n- #if $result.format == "summary":\n- --summary\n- #elif $result.format == "align":\n- --align\n- #elif $result.format == "continuous":\n- --continuous\n- #elif $result.format == "continuous-by-exon":\n- --continuous-by-exon\n- #elif $result.format == "compress":\n- --compress\n- #elif $result.format == "exons_dna":\n- --exons=cdna\n- #elif $result.format == "exons_gen":\n- --exons=genomic\n- #elif $result.format == "protein_dna":\n- --protein_dna\n- #elif $result.format == "protein_gen":\n- --protein_gen\n- #elif $result.format == "sam":\n- --format=$result.sam_paired_read\n- $result.no_sam_headers \n- #* Removed in gmap version 2011-11-30\n- #if len($result.noncanonical_splices.__str__) > 0\n- --noncanonical-splices=$result.noncanonical_splices\n- #end if\n- *#\n- #if len($result.read_group_id.__str__) > 0\n- --read-group-id=$result.read_group_id\n- #end if\n- #if len($result.read_group_name.__str__) > 0\n- --read-group-name=$result.read_group_name\n- #end if\n- #if len($result.read_group_library.__str__) > 0\n- --read-group-library=$result.read_group_library\n- #end if\n- #if len($result.read_group_platform.__str__) > 0\n- --read-group-platform=$result.read_group_platform\n- #end if\n- #elif $result.format != "gmap":\n- --format=$result.format\n- #end if\n- #if $computation.options == "advanced":\n- $computation.nosplicing\n- $computation.cross_species\n- #if len($computation.min_intronlength.__str__) > 0\n- --min-intronlength=$computation.min_intronlength\n- #end if\n- #if len($computation.intronlength.__str__) > 0\n- --intronlength=$computation.intronlength\n- #end if\n- #if len($computation.localsplicedist.__str__) > 0\n- --localsplicedist=$computation.localsplicedist\n- #end if\n- #if len($computation.totallength.__str__) > 0\n- --totallength=$computation.totallength\n- #end if\n- #if len($computation.trimendexons.__str__) > 0\n- --trimendexons=$computation.trimendexons\n- #end if\n- --direction=$computation.direction\n- --canonical-mode=$computation.canonical\n- --prunelevel=$computation.prunelevel\n- --allow-close-indels=$computation.allow_close_indels\n- #if len($computation.microexon_spliceprob.__str__) >= 0:\n- --microexon-spliceprob=$computation.microexon_spliceprob\n- #end if\n- #if len($computation.chimera_margin.__str__) >= 0:\n- --chimera-margin=$computation.chimera_margin\n- #end if\n- #end if\n- #if $advanced.options == "used":\n- #if len($advanced.npaths.__str__) > 0:\n- --npaths=$advanced.npaths\n- #end if\n- #if len($advanced.suboptimal_score.__str__) > 0:\n- --suboptimal-score=$advanced.suboptimal_score\n- #end if\n- #if len('..b'="result[\'format\']" value="gff3_match_cdna" format="gff3"/>\n- <when input="result[\'format\']" value="gff3_match_est" format="gff3"/>\n- <when input="result[\'format\']" value="sam" format="sam"/>\n- <when input="result[\'format\']" value="splicesites" format="gmap_splicesites"/>\n- <when input="result[\'format\']" value="introns" format="gmap_introns"/>\n- <when input="result[\'format\']" value="map_genes" format="gmap_annotation"/>\n- <when input="result[\'format\']" value="map_exons" format="gmap_annotation"/>\n- </change_format>\n- </data>\n- <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gmap_out.nomapping">\n- <filter>(split_output == True)</filter>\n- <change_format>\n- <when input="result[\'format\']" value="gff3_gene" format="gff3"/>\n- <when input="result[\'format\']" value="gff3_match_cdna" format="gff3"/>\n- <when input="result[\'format\']" value="gff3_match_est" format="gff3"/>\n- <when input="result[\'format\']" value="sam" format="sam"/>\n- <when input="result[\'format\']" value="splicesites" format="gmap_splicesites"/>\n- <when input="result[\'format\']" value="introns" format="gmap_introns"/>\n- <when input="result[\'format\']" value="map_genes" format="gmap_annotation"/>\n- <when input="result[\'format\']" value="map_exons" format="gmap_annotation"/>\n- </change_format>\n- </data>\n- <data format="txt" name="mult" label="${tool.name} on ${on_string} mult.${result.format}" from_work_dir="gmap_out.mult">\n- <filter>(split_output == True)</filter>\n- <change_format>\n- <when input="result[\'format\']" value="gff3_gene" format="gff3"/>\n- <when input="result[\'format\']" value="gff3_match_cdna" format="gff3"/>\n- <when input="result[\'format\']" value="gff3_match_est" format="gff3"/>\n- <when input="result[\'format\']" value="sam" format="sam"/>\n- <when input="result[\'format\']" value="splicesites" format="gmap_splicesites"/>\n- <when input="result[\'format\']" value="introns" format="gmap_introns"/>\n- <when input="result[\'format\']" value="map_genes" format="gmap_annotation"/>\n- <when input="result[\'format\']" value="map_exons" format="gmap_annotation"/>\n- </change_format>\n- </data>\n- </outputs>\n- <tests>\n- </tests> \n-\n- <help>\n-\n-**What it does**\n-\n-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. \n-\n-Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310\n-\n-.. _GMAP: http://research-pub.gene.com/gmap/\n-.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859\n-\n-------\n-\n-**Know what you are doing**\n-\n-.. class:: warningmark\n-\n-You will want to read the README_\n-\n-.. _README: http://research-pub.gene.com/gmap/src/README\n-\n- </help>\n-</tool>\n-\n' |
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| diff -r 93911bac43da -r 6adc485b6dc0 gmap_build.xml --- a/gmap_build.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,174 +0,0 @@\n-<tool id="gmap_build" name="GMAP Build" version="2.0.0">\n- <description>a database genome index for GMAP and GSNAP</description>\n- <requirements>\n- <requirement type="binary">gmap_build</requirement>\n- </requirements>\n- <version_string>gmap --version</version_string>\n- <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command>\n- <inputs>\n- <!-- Name for this gmapdb -->\n- <param name="refname" type="text" label="Name you want to give this gmap database" help="">\n- <validator type="empty_field" message="A database name is required."/>\n- </param>\n- <!-- Input data -->\n- <repeat name="inputs" title="Reference Sequence" min="1">\n- <param name="input" type="data" format="fasta" label="reference sequence fasta" />\n- </repeat>\n-\n- <param name="kmer" type="select" multiple="true" force_select="true" label="kmer size" help="">\n- <option value="12">12</option>\n- <option value="13">13</option>\n- <option value="14">14</option>\n- <option value="15" selected="true">15</option>\n- </param> \n- <param name="cmetindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create cmetindex to process reads from bisulfite-treated DNA"/>\n- <param name="atoiindex" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Create atoiindex to process reads under RNA-editing tolerance"/>\n- <conditional name="splicesite">\n- <param name="splice_source" type="select" label="Add splice and intron info from" >\n- <option value="none"></option>\n- <option value="refGeneTable">refGenes table from UCSC table browser</option>\n- <option value="gtf">GTF</option>\n- <option value="gff3">GFF3</option>\n- </param>\n- <when value="none"/>\n- <when value="refGeneTable">\n- <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" />\n- <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" \n- help="Note that alignment tracks in UCSC sometimes have an extra column on the left.">\n- <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/>\n- </param>\n- \n- </when>\n- <when value="gtf">\n- <param name="gtfGenes" type="data" format="gtf" optional="true" label="Genes as GTF" help="" />\n- </when>\n- <when value="gff3">\n- <param name="gff3Genes" type="data" format="gff3" optional="true" label="Genes in GFF3 format" help="" />\n- </when>\n- </conditional> \n- <conditional name="dbsnp">\n- <param name="snp_source" type="select" label="Add SNP info from" >\n- <option value="none"></option>\n- <option value="snpTable">UCSC SNP Table</option>\n- <option value="snpFile">GMAP SNP File</option>\n- </param>\n- <when value="none"/>\n- <when value="snpTable">\n- <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" />\n- <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" />\n- <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">\n- <option value="1" selected="true">1 (High)</option>\n- <option value="2">2 (Medium)</option>\n- <option value="3">3 (All)</option>\n- </param>\n- </when>\n- <when value="snpFile">\n- <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file" \n- help="Format (3 columns):\n- <br>>rs62211261 21:14379270 CG\n- <br>>rs62211262 2'..b' to the possible nucleotides on the plus strand of the genome. \n- If the one of these two letters does not match the allele in the reference\n- sequence, that SNP will be ignored in subsequent processing as a probable error.\n- The N stands for any other allele." />\n- </when>\n- </conditional> \n- </inputs>\n- <outputs>\n- <!--\n- <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>\n- -->\n- <data format="gmapdb" name="output" label="${tool.name} on ${on_string} gmapdb ${refname}" />\n- </outputs>\n- <configfiles>\n- <configfile name="shscript">\n-#!/bin/bash\n-#set $ds = chr(36)\n-#set $gt = chr(62)\n-#set $lt = chr(60)\n-#set $ad = chr(38)\n-## #set $ref_files = \'\'\n-## #for $i in $inputs:\n- ## #set $ref_files = $ref_files $i.input\n-## #end for\n-## echo $ref_files\n-#import os.path\n-#set $gmapdb = $output.extra_files_path\n-#set $mapsdir = $os.path.join($os.path.join($gmapdb,str($refname)), str($refname) + \'.maps\')\n-mkdir -p $gmapdb\n-## export GMAPDB required for cmetindex and atoiindex\n-export GMAPDB=$gmapdb\n-#for $k in $kmer.__str__.split(\',\'):\n-gmap_build -D $gmapdb -d $refname -s numeric-alpha -k $k #for i in $inputs# ${i.input}#end for#\n-#end for\n-get-genome -D $gmapdb -d \'?\' | sed \'s/^Available .*/gmap db: /\' \n-echo "kmers: " $kmer \n-#if $splicesite.splice_source == \'refGeneTable\':\n-#if $splicesite.refGenes.__str__ != \'None\':\n-cat $splicesite.refGenes | psl_splicesites -s $splicesite.col_skip | iit_store -o $os.path.join($mapsdir,\'splicesites\')\n-cat $splicesite.refGenes | psl_introns -s $splicesite.col_skip | iit_store -o $os.path.join($mapsdir,\'introns\')\n-#end if\n-#elif $splicesite.splice_source == \'gtf\':\n-#if $splicesite.gtfGenes.__str__ != \'None\':\n-cat $splicesite.gtfGenes | gtf_splicesites | iit_store -o $os.path.join($mapsdir,\'splicesites\')\n-cat $splicesite.gtfGenes | gtf_introns | iit_store -o $os.path.join($mapsdir,\'introns\')\n-#end if\n-#elif $splicesite.splice_source == \'gff3\':\n-#if $splicesite.gff3Genes.__str__ != \'None\':\n-cat $splicesite.gff3Genes | gff3_splicesites | iit_store -o $os.path.join($mapsdir,\'splicesites\')\n-cat $splicesite.gff3Genes | gff3_introns | iit_store -o $os.path.join($mapsdir,\'introns\')\n-#end if\n-#end if\n-#if $dbsnp.snp_source != \'none\' and $dbsnp.snps.__str__ != \'None\':\n-#if $dbsnp.snp_source == \'snpTable\':\n-#if $dbsnp.snpsex.__str__ != \'None\':\n-cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight -e $dbsnp.snpsex | iit_store -o $os.path.join($mapsdir,\'snps\')\n-#else:\n-cat $dbsnp.snps | dbsnp_iit -w $dbsnp.weight | iit_store -o $os.path.join($mapsdir,\'snps\')\n-#end if\n-#else:\n-cat $dbsnp.snps | iit_store -o $os.path.join($mapsdir,\'snps\')\n-#end if\n-snpindex -d $refname -v snps\n-echo "snpindex" -d $refname -v snps\n-#end if\n-#if $cmetindex.__str__ == \'yes\':\n-cmetindex -d $refname\n-echo "cmetindex" -d $refname\n-#end if\n-#if $atoiindex.__str__ == \'yes\':\n-atoiindex -d $refname\n-echo "atoiindex" -d $refname\n-#end if\n-get-genome -D $gmapdb -d $refname -m \'?\' | sed \'s/^Available maps .*/maps: /\' \n- </configfile>\n- </configfiles>\n-\n- <tests>\n- </tests> \n-\n- <help>\n-\n-\n-**GMAP Build**\n-\n-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.)\n-\n-You will want to read the README_\n-\n-Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310\n-\n-.. _GMAP: http://research-pub.gene.com/gmap/\n-.. _GSNAP: http://research-pub.gene.com/gmap/\n-.. _README: http://research-pub.gene.com/gmap/src/README\n-.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859\n-\n-\n- </help>\n-</tool>\n-\n' |
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| diff -r 93911bac43da -r 6adc485b6dc0 gsnap.xml --- a/gsnap.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,864 +0,0 @@\n-<tool id="gsnap" name="GSNAP" version="2.0.1">\n- <description>Genomic Short-read Nucleotide Alignment Program</description>\n- <requirements>\n- <requirement type="binary">gsnap</requirement>\n- </requirements>\n- <version_string>gsnap --version</version_string>\n- <command>\n- #import os.path, re\n- gsnap\n- --nthreads="4" --ordered\n- #if $refGenomeSource.genomeSource == "gmapdb":\n- #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0]\n- --dir=$refGenomeSource.gmapdb.extra_files_path --db=$refGenomeSource.gmapdb.metadata.db_name\n- #else:\n- --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value)\n- #end if\n- #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:\n- --kmer=$refGenomeSource.kmer\n- #end if\n- #if $refGenomeSource.use_splicing.src == \'gmapdb\':\n- #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:\n- -s $refGenomeSource.use_splicing.splicemap.value\n- #if $computation.trim_mismatch_score.__str__ == \'0\':\n- $ambig_splice_noclip\n- #end if\n- #end if\n- #elif $refGenomeSource.use_splicing.src == \'history\':\n- #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:\n- -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap)\n- #if $computation.trim_mismatch_score.__str__ == \'0\':\n- $ambig_splice_noclip\n- #end if\n- #end if\n- #end if\n- #if $refGenomeSource.use_snps.src == \'gmapdb\':\n- #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0:\n- -v $refGenomeSource.use_snps.snpindex.value\n- #end if\n- #elif $refGenomeSource.use_snps.src == \'history\':\n- #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0:\n- -V $refGenomeSource.use_snps.snpindex.extra_files_path -v $refGenomeSource.use_snps.snpindex.metadata.snps_name\n- #end if\n- #end if\n- #if $refGenomeSource.mode.__str__ != \'\':\n- --mode=$refGenomeSource.mode\n- #end if\n- #* ## No longer in options as of version 2011-11-30\n- #if $mapq_unique_score.__str__ != \'\':\n- --mapq-unique-score=$mapq_unique_score\n- #end if\n- *#\n- #if $computation.options == "advanced":\n- #if $computation.max_mismatches.__str__ != \'\':\n- --max-mismatches=$computation.max_mismatches\n- #end if\n- $computation.query_unk_mismatch\n- $computation.genome_unk_mismatch\n- #if $computation.terminal_threshold.__str__ != \'\':\n- --terminal-threshold=$computation.terminal_threshold\n- #end if\n- #if $computation.indel_penalty.__str__ != \'\':\n- --indel-penalty=$computation.indel_penalty\n- #end if\n- #if $computation.indel_endlength.__str__ != \'\':\n- --indel-endlength=$computation.indel_endlength\n- #end if\n- #if $computation.max_middle_insertions.__str__ != \'\':\n- --max-middle-insertions=$computation.max_middle_insertions\n- #end if\n- #if $computation.max_middle_deletions.__str__ != \'\':\n- --max-middle-deletions=$computation.max_middle_deletions\n- #end if\n- #if $computation.max_end_insertions.__str__ != \'\':\n- --max-end-insertions=$computation.max_end_insertions\n- #end if\n- #if $computation.max_end_deletions.__str__ != \'\':\n- --max-end-deletions=$computation.max_end_deletions\n- #end if\n- #if $computation.suboptimal_levels.__str__ != \'\':\n- --suboptimal-levels=$computation.suboptimal_levels\n- #end if\n- #if $computation.adapter_strip.__str__ != \'\':\n- --adapter-strip=$computation.adapter_strip\n- #end if\n- #if $computation.trim_mismatch_score.__str__ != \'\':\n- '..b'value="sam" format="sam"/>\n- <when input="result[\'format\']" value="gsnap" format="gsnap"/>\n- </change_format>\n- </data>\n-\n- <data format="fastq" name="nomapping_fq" label="${tool.name} on ${on_string} nomapping.fq" from_work_dir="gsnap_out.nomapping.fq">\n- <filter>(results[\'split_output\'] == \'yes\' and seq[\'format\'] == \'fastq\' and seq[\'paired\'][\'ispaired\'] == False)</filter>\n- </data>\n-\n- <data format="fastq" name="nomapping_1_fq" label="${tool.name} on ${on_string} nomapping.1.fq" from_work_dir="gsnap_out.nomapping.1.fq">\n- <filter>(results[\'split_output\'] == \'yes\' and seq[\'format\'] == \'fastq\' and seq[\'paired\'][\'ispaired\'] == True)</filter>\n- </data>\n-\n- <data format="fastq" name="nomapping_2_fq" label="${tool.name} on ${on_string} nomapping.2.fq" from_work_dir="gsnap_out.nomapping.2.fq">\n- <filter>(results[\'split_output\'] == \'yes\' and seq[\'format\'] == \'fastq\' and seq[\'paired\'][\'ispaired\'] == True)</filter>\n- </data>\n-\n- <!-- Will problay need wrapper code to generate composite datatype for goby alignment\n- <data format="gobyalignment" name="goby_alignment" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.nomapping">\n- <filter>result[\'format\'] == \'goby\'</filter>\n- </data>\n- -->\n-\n- </outputs>\n- <tests>\n- </tests> \n-\n- <help>\n-\n-**What it does**\n-\n-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. \n-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.\n-\n-.. _GSNAP: http://research-pub.gene.com/gmap/\n-.. _Publication: http://bioinformatics.oupjournals.org/cgi/content/full/26/7/873\n-http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844994/?tool=pubmed\n-\n-------\n-\n-**Know what you are doing**\n-\n-.. class:: warningmark\n-\n-You will want to read the README_\n-\n-.. _README: http://research-pub.gene.com/gmap/src/README\n-\n-------\n-\n-**Input formats**\n-\n-Input to GSNAP should be either in FASTQ or FASTA format. \n-\n-The FASTQ input may include quality scores, which will then be included in SAM\n-output, if that output format is selected. \n-\n-For FASTA format, you should include one line per read (or end of a\n-paired-end read). The same FASTA file can have a mixture of\n-single-end and paired-end reads of varying lengths, if desired.\n-\n-Single-end reads:\n-\n-Each FASTA entry should contain one short read per line, like this\n-\n->Header information\n-AAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTA\n-\n-Each short read can have a different length. However, the entire read\n-needs to be on a single line, and may not wrap around multiple lines.\n-If it extends to a second line, GSNAP will think that the read is\n-paired-end.\n-\n-\n-Paired-end reads:\n-\n-Each FASTA entry should contain two short reads, one per line, like\n-this\n-\n->Header information\n-AAAACATTCTCCTCCGCATAAGCCTAGTAGATTA\n-GGCGTAGGTAGAAGTAGAGGTTAAGGCGCGTCAG\n-\n-By default, the program assumes that the second end is in the reverse\n-complement direction compared with the first end. If they are in the\n-same direction, you may need to use the --circular-input (or -c) flag.\n-\n-( The Galaxy tool: "FASTA Width formatter" can be used to reformat fasta files to have single line sequences. )\n-\n-------\n-\n-**Output formats in GSNAP**\n-\n-SAM output format\n-\n-Default GSNAP format\n- See the README_\n-\n-\n-\n-\n- </help>\n-</tool>\n-\n' |
| b |
| diff -r 93911bac43da -r 6adc485b6dc0 iit_store.xml --- a/iit_store.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,181 +0,0 @@\n-<tool id="gmap_iit_store" name="GMAP IIT" version="2.0.0">\n- <description>Create a map store for known genes or SNPs</description>\n- <requirements>\n- <requirement type="binary">iit_store</requirement>\n- </requirements>\n- <version_string>iit_store --version</version_string>\n- <command interpreter="command"> /bin/bash $shscript 2> $log </command>\n- <inputs>\n- <!-- Input data -->\n- <conditional name="map">\n- <param name="type" type="select" label="Make map for" >\n- <option value="genes">Introns and Splice sites</option>\n- <option value="snps">SNPs</option>\n- <option value="gmap">GMAP Annotation</option>\n- </param>\n- <when value="genes">\n- <conditional name="src">\n- <param name="src_format" type="select" label="Add splice and intron info from" >\n- <option value="refGeneTable">refGenes table from UCSC table browser</option>\n- <option value="gtf">GTF</option>\n- <option value="gff3">GFF3</option>\n- </param>\n- <when value="refGeneTable">\n- <param name="genes" type="data" format="tabular" label="UCSC refGenes table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz" />\n- <param name="col_skip" type="integer" value="1" label="Columns to skip before the id/name column (default 1)" \n- help="Note that alignment tracks in UCSC sometimes have an extra column on the left.">\n- <validator type="in_range" message="The number of colmumns to skip must >= 0." min="0."/>\n- </param>\n- </when>\n- <when value="gtf">\n- <param name="genes" type="data" format="gtf" label="Genes as GTF" help="" />\n- </when>\n- <when value="gff3">\n- <param name="genes" type="data" format="gff3" label="Genes in GFF3 format" help="" />\n- </when>\n- </conditional> \n- <param name="maps" type="select" display="checkboxes" multiple="true" force_select="true" label="Add splice and intron info from" >\n- <option value="splicesites" selected="true">splicesites.iit</option>\n- <option value="introns" selected="false">introns.iit</option>\n- </param>\n- </when>\n- <when value="snps">\n- <conditional name="src">\n- <param name="src_format" type="select" label="Add SNP info from" >\n- <option value="snpTable">UCSC SNP Table</option>\n- <option value="snpFile">GMAP SNP File</option>\n- </param>\n- <when value="snpTable">\n- <param name="snps" type="data" format="tabular" label="UCSC SNPs table" help="Example: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/snp130.txt.gz" />\n- <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" />\n- <param name="weight" type="select" label="Include SNPs with at least Confidence Level" help="">\n- <option value="1" selected="true">1 (High)</option>\n- <option value="2">2 (Medium)</option>\n- <option value="3">3 (All)</option>\n- </param>\n- </when>\n- <when value="snpFile">\n- <param name="snps" type="data" format="gmap_snps" optional="true" label="GMAP SNPs file" \n- help="Format (3 columns):<B>\n- <br>>rs62211261 21:14379270 CG\n- <br>>rs62211262 21:14379281 CG\n- </B>\n- <br>Each line must start with a > character, then be followed by an\n- identifier (which may have duplicates). Then there should be the\n- chromosomal coordinate of the SNP. (Coordinates are all 1-based, so\n- the first character of a chromosome is number 1.) Finally, there\n- '..b'- <br> chr:position\n- <br> chr:startposition..endposition\n- <br>The term chr:position is equivalent to chr:position..position. \n- <br>If you want to indicate that the interval is on the minus strand or reverse direction, then endposition may be less than startposition. \n- " />\n- </when>\n- </conditional> \n- </inputs>\n- <outputs>\n- <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>\n- <data format="splicesites.iit" name="splicesites_iit" label="${tool.name} on ${on_string} splicesites.iit">\n- <filter>(map[\'type\'] == \'genes\' and \'splicesites\' in map[\'maps\'])</filter>\n- </data>\n- <data format="introns.iit" name="introns_iit" label="${tool.name} on ${on_string} introns.iit">\n- <filter>(map[\'type\'] == \'genes\' and \'introns\' in map[\'maps\'])</filter>\n- </data>\n- <data format="snps.iit" name="snps_iit" label="${tool.name} on ${on_string} snps.iit">\n- <filter>(map[\'type\'] == \'snps\')</filter>\n- </data>\n- <data format="iit" name="map_iit" label="${tool.name} on ${on_string} map.iit">\n- <filter>(map[\'type\'] == \'gmap\')</filter>\n- </data>\n- </outputs>\n- <configfiles>\n- <configfile name="shscript">\n-#!/bin/bash\n-#set $catcmd = \'gzcat -f\'\n-#set $catcmd = \'cat\'\n-#set $ds = chr(36)\n-#set $gt = chr(62)\n-#set $lt = chr(60)\n-#set $ad = chr(38)\n-#set $ep = chr(33)\n-#set $toerr = \'\'.join([$gt,$ad,\'2\'])\n-#import os.path\n-#if $map.type == \'genes\':\n-if [ $ep -e $map.src.genes ]; then echo "$map.src.genes does not exist" $toerr; exit 1; fi\n-if [ $ep -s $map.src.genes ]; then echo "$map.src.genes is empty" $toerr; exit 2; fi\n- #if $map.src.src_format == \'refGeneTable\':\n- #if \'splicesites\' in [ $map.maps.__str__ ]:\n- $catcmd $map.src.genes | psl_splicesites -s $map.src.col_skip | iit_store -o $splicesites_iit\n- #end if\n- #if \'introns\' in [ $map.maps.__str__ ]:\n- $catcmd $map.src.genes | psl_introns -s $map.src.col_skip | iit_store -o $introns_iit\n- #end if\n- #elif $map.src.src_format == \'gtf\':\n- #if \'splicesites\' in [ $map.maps.__str__ ]:\n- $catcmd $map.src.genes | gtf_splicesites | iit_store -o $splicesites_iit\n- #end if\n- #if \'introns\' in [ $map.maps.__str__ ]:\n- $catcmd $map.src.genes | gtf_introns | iit_store -o $introns_iit\n- #end if\n- #elif $map.src.src_format == \'gff3\':\n- #if \'splicesites\' in [ $map.maps.__str__ ]:\n- $catcmd $map.src.genes | gff3_splicesites | iit_store -o $splicesites_iit\n- #end if\n- #if \'introns\' in [ $map.maps.__str__ ]:\n- $catcmd $map.src.genes | gff3_introns | iit_store -o $introns_iit\n- #end if\n- #end if\n-#elif $map.type == \'snps\':\n-if [ $ep -s $map.src.snps ]; then echo "$map.src.snps is empty" $toerr; exit 2; fi\n- #if $map.src.snpsex.__str__ != \'None\':\n- $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight -e $map.src.snpsex | iit_store -o $snps_iit\n- #else:\n- $catcmd $map.src.snps | dbsnp_iit -w $map.src.weight | iit_store -o $snps_iit \n- #end if\n-#else:\n- $catcmd $map.src.snps | iit_store -o $map_iit \n-#end if\n- </configfile>\n- </configfiles>\n-\n- <tests>\n- </tests> \n-\n- <help>\n-\n-\n-**iit_store**\n-\n-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. \n-\n-You will want to read the README_\n-\n-Publication_ citation: Thomas D. Wu, Colin K. Watanabe Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310\n-\n-.. _GMAP: http://research-pub.gene.com/gmap/\n-.. _GSNAP: http://research-pub.gene.com/gmap/\n-.. _README: http://research-pub.gene.com/gmap/src/README\n-.. _Publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/21/9/1859\n-\n-\n-**inputs**\n-\n- </help>\n-</tool>\n-\n' |
| b |
| diff -r 93911bac43da -r 6adc485b6dc0 lib/galaxy/datatypes/gmap.py --- a/lib/galaxy/datatypes/gmap.py Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,472 +0,0 @@\n-"""\n-GMAP indexes\n-"""\n-import logging\n-import os,os.path,re\n-import galaxy.datatypes.data\n-from galaxy.datatypes.data import Text\n-from galaxy import util\n-from galaxy.datatypes.metadata import MetadataElement\n-\n-log = logging.getLogger(__name__)\n-\n-class GmapDB( Text ):\n- """\n- A GMAP DB for indexes\n- """\n- MetadataElement( name="db_name", desc="The db name for this index set", default=\'unknown\', set_in_upload=True, readonly=True )\n- MetadataElement( name="basesize", default="12", desc="The basesize for offsetscomp", visible=True, readonly=True )\n- MetadataElement( name="kmers", default=[\'\'], desc="The kmer sizes for indexes", visible=True, no_value=[\'\'], readonly=True )\n- MetadataElement( name="map_dir", desc="The maps directory", default=\'unknown\', set_in_upload=True, readonly=True )\n- MetadataElement( name="maps", default=[\'\'], desc="The names of maps stored for this gmap gmapdb", visible=True, no_value=[\'\'], readonly=True )\n- MetadataElement( name="snps", default=[\'\'], desc="The names of SNP indexes stored for this gmapdb", visible=True, no_value=[\'\'], readonly=True )\n- MetadataElement( name="cmet", default=False, desc="Has a cmet index", visible=True, readonly=True )\n- MetadataElement( name="atoi", default=False, desc="Has a atoi index", visible=True, readonly=True )\n- \n- file_ext = \'gmapdb\'\n- is_binary = True\n- composite_type = \'auto_primary_file\'\n- allow_datatype_change = False\n-\n- def generate_primary_file( self, dataset = None ):\n- """ \n- This is called only at upload to write the html file\n- cannot rename the datasets here - they come with the default unfortunately\n- """\n- return \'<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>\'\n- \n- def regenerate_primary_file(self,dataset):\n- """\n- cannot do this until we are setting metadata \n- """\n- bn = dataset.metadata.db_name\n- log.info( "GmapDB regenerate_primary_file %s" % (bn))\n- 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)]\n- for i,name in enumerate(dataset.metadata.maps):\n- rval.append( \'<li>%s\' % name)\n- rval.append( \'</ul></html>\' )\n- f = file(dataset.file_name,\'w\')\n- f.write("\\n".join( rval ))\n- f.write(\'\\n\')\n- f.close()\n-\n- def set_peek( self, dataset, is_multi_byte=False ):\n- log.info( "GmapDB set_peek %s" % (dataset))\n- if not dataset.dataset.purged:\n- 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 )\n- dataset.blurb = "GMAPDB %s" % ( dataset.metadata.db_name )\n- else:\n- dataset.peek = \'file does not exist\'\n- dataset.blurb = \'file purged from disk\'\n- def display_peek( self, dataset ):\n- try:\n- return dataset.peek\n- except:\n- return "GMAP index file"\n-\n- def sniff( self, filename ):\n- return False\n- def set_meta( self, dataset, overwrite = True, **kwd ):\n- """\n- Expecting:\n- extra_files_path/<db_name>/db_name>.ref<basesize><kmer>3<index>\n- extra_files_path/db_name/db_name.ref1[2345]1[2345]3offsetscomp\n- extra_files_path/db_name/db_name.ref1[2345]1[2345]3positions\n- extra_files_path/db_name/db_name.ref1[2345]1[2345]3gammaptrs\n- index maps: \n- extra_files_path/db_name/db_name.maps/*.iit\n- """\n- log.info( "GmapDB set_meta %s %s" % (dataset,dataset.extra_files_path))\n- pat = \'(.*)\\.((ref)|(met)[atgc][atgc]|(a2i)[atgc][atgc])((\\d\\d)(\\d\\d))?3positions(\\.(.+))?\'\n- efp = dataset.extra_files_path\n- flist = os.listdir(efp)\n- for i,fname in enumerate(flist):\n- log.info( "GmapDB'..b' == None: # Failed to match \n- return False\n- finally:\n- fh.close()\n- return False\n-\n-class SNPAnnotation(IntervalAnnotation):\n- file_ext = \'gmap_snps\'\n- """\n- Example:\n- >rs62211261 21:14379270 CG\n- >rs62211262 21:14379281 AT\n- >rs62211263 21:14379298 WN\n- Each line must start with a ">" character, then be followed by an\n- identifier (which may have duplicates). Then there should be the\n- chromosomal coordinate of the SNP. (Coordinates are all 1-based, so\n- the first character of a chromosome is number 1.) Finally, there\n- should be the two possible alleles. (Previous versions required that\n- these be in alphabetical order: "AC", "AG", "AT", "CG", "CT", or "GT",\n- but that is no longer a requirement.) These alleles must correspond\n- to the possible nucleotides on the plus strand of the genome. If the\n- one of these two letters does not match the allele in the reference\n- sequence, that SNP will be ignored in subsequent processing as a\n- probable error.\n- \n- GSNAP also supports the idea of a wildcard SNP. A wildcard SNP allows\n- all nucleotides to match at that position, not just a given reference\n- and alternate allele. It is essentially as if an "N" were recorded at\n- that genomic location, although the index files still keep track of\n- the reference allele. To indicate that a position has a wildcard SNP,\n- you can indicate the genotype as "WN", where "W" is the reference\n- allele. Another indication of a wildcard SNP is to provide two\n- separate lines at that position with the genotypes "WX" and "WY",\n- where "W" is the reference allele and "X" and "Y" are two different\n- alternate alleles.\n- """\n- def sniff( self, filename ):\n- """\n- Determines whether the file is a gmap SNP annotation file\n- """\n- try:\n- pat = \'>(\\S+)\\s((\\S+):(\\d+)\\s([TACGW][TACGN])$\' #>label chr:position ATCG \n- fh = open( filename )\n- count = 0\n- while True and count < 10:\n- line = fh.readline()\n- if not line:\n- break #EOF\n- line = line.strip()\n- if line: #first non-empty line\n- count += 1\n- if re.match(pat,line) == None: # Failed to match \n- return False\n- finally:\n- fh.close()\n- return False\n-\n-\n-class TallyAnnotation(IntervalAnnotation):\n- file_ext = \'gsnap_tally\'\n- """\n- Output produced by gsnap_tally\n- Example:\n- >144 chr20:57268791..57268935\n- G0\n- A1(1@7|1Q-3)\n- A2(1@36,1@1|1Q2,1Q-8)\n- 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\n- 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\n- """\n- def sniff( self, filename ): # TODO\n- """\n- Determines whether the file is a gmap splice site annotation file\n- """\n- try:\n- pat = \'^>(\\d+)\\s((\\S+):(\\d+)\\.\\.(\\d+))$\' #>total chr:position..position\n- pat2 = \'^[GATCN]\\d.*$\' #BaseCountDeatails\n- fh = open( filename )\n- count = 0\n- while True and count < 10:\n- line = fh.readline()\n- if not line:\n- break #EOF\n- line = line.strip()\n- if line: #first non-empty line\n- count += 1\n- if re.match(pat,line) == None and re.match(pat2,line) == None: # Failed to match \n- return False\n- finally:\n- fh.close()\n- return False\n-\n-class GsnapResult( Text ):\n- """\n- The default output format for gsnap. Can be used as input for gsnap_tally.\n- """\n- file_ext = \'gsnap\'\n-\n-\n' |
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| diff -r 93911bac43da -r 6adc485b6dc0 snpindex.xml --- 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> - |
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| diff -r 93911bac43da -r 6adc485b6dc0 tool-data/datatypes_conf.xml --- a/tool-data/datatypes_conf.xml Thu Jan 05 14:31:24 2012 -0600 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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> |
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| diff -r 93911bac43da -r 6adc485b6dc0 tool-data/gmap_indices.loc.sample --- 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 |
| b |
| @@ -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 |
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| diff -r 93911bac43da -r 6adc485b6dc0 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jul 31 08:19:46 2012 -0400 |
| b |
| @@ -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> |