Mercurial > repos > jjohnson > gmap
diff gmap_build.xml @ 11:6adc485b6dc0 draft default tip
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| author | jjohnson |
|---|---|
| date | Tue, 31 Jul 2012 08:19:46 -0400 |
| parents | 93911bac43da |
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--- 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> -