Mercurial > repos > yusuf > generate_genomeid

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initial commit for genomeid tool
author Yusuf Ali <ali@yusuf.email>
date Thu, 12 Mar 2015 09:49:46 -0600
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1 <?xml version="1.0" ?>
2
3 <tool id="generate_genomeid" name='Generate GenomeID' version='1.0.0' hidden='false'>
4
5 <command interpreter="perl">
6 generateID.pl --o $genomeID --n $noise --hg $hg --b $baq --s $sex --u $ucn --r $ref
7 #if $source.source_select=="bam"
8 --type bam --file $bamFile
9 #elif $source.source_select=="vcf"
10 --type vcf --file $vcfFile
11 #else
12 --type tbi --file $tbi_gz
13 #end if
14 #if $sampleName
15 --sN $sampleName
16 #end if
17
18 </command>
19
20 <inputs>
21 <conditional name="source">
22 <param name="source_select" type="select" label="Sequence Source Type">
23 <option value="bam">Binary Alignment Map (BAM)</option>
24 <option value="vcf">Variant Call Format (VCF)</option>
25 <option value="tbi">Indexed TAB-delimited (TABIX)</option>
26 </param>
27
28 <when value="bam">
29 <param name="bamFile" type="data" format="bam" label="BAM file" help="If file is not listed, ensure it is set to bam datatype"></param>
30 </when>
31
32 <when value="vcf">
33 <param name="vcfFile" type="data" format="vcf" label="VCF File" help="If file is not listed, ensure it is set to vcf datatype"></param>
34 </when>
35
36 <when value="tbi">
37 <param name="tbi_gz" type="data" format="vcf_bgzip" label="Compressed VCF File" help="If file is not listed, ensure it is set to vcf_bgzip datatype"></param>
38 </when>
39
40 </conditional>
41
42 <param name="hg" type="select" label="Version of the reference Human Genome" help="Warning: Selection of Unknown may return a poor identifier">
43 <option value="hg19">Human Genome Version 19</option>
44 <option value="hg38">Human Genome Version 38</option>
45 <option value="none">Unknown</option>
46 </param>
47
48 <param name="sampleName" type="text" label="Name of the sample" help="Used if source file contains more than one sample"></param>
49 <param name="noise" type="float" value="0.05" label="Threshold for maximum allowed noise"></param>
50 <param name="baq" type="integer" value="30" label=""></param>
51 <param name="sex" type="boolean" checked="true" label="Include Sex Chromosome Information"></param>
52 <param name="ucn" type="boolean" checked="false" label="Sample has unusual copy number"></param>
53 <param name="ref" type="boolean" checked="false" label="Match to reference geneome if marker not found"></param>
54
55 </inputs>
56
57 <outputs>
58 <data name="genomeID" format="txt" label="${sampleName}_genomeID" />
59 </outputs>
60 </tool>