Mercurial > repos > jjohnson > gmap
diff snpindex.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/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> -