Mercurial > repos > yusuf > generate_genomeid
changeset 0:7e4eb6957b8a default tip
initial commit for genomeid tool
| author | Yusuf Ali <ali@yusuf.email> |
|---|---|
| date | Thu, 12 Mar 2015 09:49:46 -0600 |
| parents | |
| children | |
| files | generateID.pl genomeid.xml |
| diffstat | 2 files changed, 106 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generateID.pl Thu Mar 12 09:49:46 2015 -0600 @@ -0,0 +1,46 @@ +#!/usr/bin/perl + +use strict; +use warnings; +use Getopt::Long; + +use Bio::Seq::GenomeID qw(generate_id); + +my ($outFile, $inFile, $type, $index, $hg); +my ($noise, $baq, $sex, $ucn, $ref, $name); + +GetOptions("o=s"=> \$outFile, + "n=f"=>\$noise, + "hg=s"=> \$hg, + "b=i"=> \$baq, + "s=s"=> \$sex, + "u=s"=> \$ucn, + "r=s"=> \$ref, + "type=s"=> \$type, + "file=s"=> \$inFile, + "sN=s"=> \$name, +); +$ucn = ($ucn eq "true")? 1:0; $sex = ($sex eq "true")?1:0; $ref = ($ref eq "true")?1:0; + +my %obj; +$obj{'type'} = $type; $obj{'file'} = $inFile; +$obj{'ucn'} = $ucn; $obj{'sex'} = $sex; $obj{'ref'} = $ref; +$obj{'noise'} = $noise; $obj{'baq'} = $baq; + +if($type eq "tbi"){ + `tabix -p vcf $inFile`; +} + + +if($hg ne "none"){ + $obj{'hg'} = $hg; +} + +if( defined $name ){ + $obj{'sampleName'} = $name; +} + +my $genomeID = generate_id(%obj); +open(my $fh, '>', $outFile); +print $fh $genomeID; +close $fh;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/genomeid.xml Thu Mar 12 09:49:46 2015 -0600 @@ -0,0 +1,60 @@ +<?xml version="1.0" ?> + +<tool id="generate_genomeid" name='Generate GenomeID' version='1.0.0' hidden='false'> + + <command interpreter="perl"> + generateID.pl --o $genomeID --n $noise --hg $hg --b $baq --s $sex --u $ucn --r $ref + #if $source.source_select=="bam" +--type bam --file $bamFile + #elif $source.source_select=="vcf" +--type vcf --file $vcfFile + #else +--type tbi --file $tbi_gz + #end if + #if $sampleName +--sN $sampleName + #end if + + </command> + + <inputs> + <conditional name="source"> + <param name="source_select" type="select" label="Sequence Source Type"> + <option value="bam">Binary Alignment Map (BAM)</option> + <option value="vcf">Variant Call Format (VCF)</option> + <option value="tbi">Indexed TAB-delimited (TABIX)</option> + </param> + + <when value="bam"> + <param name="bamFile" type="data" format="bam" label="BAM file" help="If file is not listed, ensure it is set to bam datatype"></param> + </when> + + <when value="vcf"> + <param name="vcfFile" type="data" format="vcf" label="VCF File" help="If file is not listed, ensure it is set to vcf datatype"></param> + </when> + + <when value="tbi"> + <param name="tbi_gz" type="data" format="vcf_bgzip" label="Compressed VCF File" help="If file is not listed, ensure it is set to vcf_bgzip datatype"></param> + </when> + + </conditional> + + <param name="hg" type="select" label="Version of the reference Human Genome" help="Warning: Selection of Unknown may return a poor identifier"> + <option value="hg19">Human Genome Version 19</option> + <option value="hg38">Human Genome Version 38</option> + <option value="none">Unknown</option> + </param> + + <param name="sampleName" type="text" label="Name of the sample" help="Used if source file contains more than one sample"></param> + <param name="noise" type="float" value="0.05" label="Threshold for maximum allowed noise"></param> + <param name="baq" type="integer" value="30" label=""></param> + <param name="sex" type="boolean" checked="true" label="Include Sex Chromosome Information"></param> + <param name="ucn" type="boolean" checked="false" label="Sample has unusual copy number"></param> + <param name="ref" type="boolean" checked="false" label="Match to reference geneome if marker not found"></param> + + </inputs> + + <outputs> + <data name="genomeID" format="txt" label="${sampleName}_genomeID" /> + </outputs> +</tool>