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