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comparison vcftools.xml @ 3:0bef79a36ae1 draft

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author nilesh
date Wed, 10 Jul 2013 17:19:39 -0400
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1 <toold id="vcftools" name="VCFtools" version="0.0.1">
2 <description>
3 The vcftools program is intended for analysis of diploid SNP data in VCF format.
4 </description>
5 <requirements>
6 <requirement type="package" version="0.1.11">vcftools</requirement>
7 </requirements>
8 <command>
9 vcftools
10
11 #if str($basic) == "gzvcf"
12 --gzvcf
13 #elif str($basic) == "bcf"
14 --bcf
15 #else
16 --vcf
17 #end if
18
19 $input
20
21 #for $chromosome in $chr
22 --chr $chromosome.number
23 #end for
24
25 #for $chromosome in $notchr
26 --notchr $chromosome.number
27 #end for
28
29 #if str($frombp) != ""
30 --from-bp $frombp
31 #end if
32
33 #if str($tobp) != ""
34 --to-bp $tobp
35 #end if
36
37 #for $snp in $snps
38 --snp $snp.id
39 #end for
40
41 #if str(${snpfile.file_name}) != ""
42 --snps $snpfile
43 #end if
44
45 #if str(${excludesnpfile.file_name}) != ""
46 --snps $excludesnpfile
47 #end if
48
49 #if str($indels) == "keeponlyindels"
50 --keep-only-indels
51 #elif str($indels) == "removeindels"
52 --removeindels
53 #end if
54
55 $removefilterall $recodetostream > out.recode.vcf
56 </command>
57 <inputs>
58 <param name="input" type="data" label="Input vcf file" format="vcf" />
59 <param name="basic" type="select" label="Basic Options" value="vcf">
60 <option value="vcf">Decompressed vcf file (default)</option>
61 <option value="gzvcf">Compressed (gzipped) vcf file</option>
62 <option value="bcf">Compressed (bgzf) bcf file</option
63 </param>
64 <repeat name="chr" title="Include chromosomes to be processed">
65 <param name="number" label="Chromosome number" type="integer" optional="true" />
66 </repeat>
67 <repeat name="notchr" title="Exclude chromosomes from processing">
68 <param name="number" label="Chromosome number" type="integer" optional="true" />
69 </repeat>
70 <param name="frombp" label="Beginning of range to be processed" help="only if chromosomes are included. You must also specify the end of range to be processed." optional="true" type="integer"/>
71 <param name="tobp" label="End of range to be processed" optional="true" type="integer" help="only if chromosomes are included. You must also specify the beginning of range to be processed."/>
72 <repeat name="snps" title="SNPs to include">
73 <param name="id" label="ID of SNP" type="text" optional="true" help="e.g. a dbSNP rsID"/>
74 </repeat>t
75 <param name="snpfile" type="data" format="txt, tabular" label="List of SNPs to include" help="The file should contain a list of SNP IDs (e.g. dbSNP rsIDs), with one ID per line." optional="true"/>
76 <param name="excludesnpfile" type="data" label = "List of SNPs to disclude" format="txt, tabular" help="The file should contain a list of SNP IDs (e.g. dbSNP rsIDs), with one ID per line." optional="true"/>
77 <param name="indels" type="select" label="Indel options" value="none">
78 <option value="keeponlyindels">Keep only indels</option>
79 <option value="removeindels"> Remove indels</option>
80 </param>
81 <param name="removefilterall" type="boolean" truevalue="--remove-filtered-all" falsevalue="" label="Remove all sites with the FILTER tag" value="false" />
82 <param name="recodetostream" type="boolean" truevalue="--recode-to-stream" falsevalue="" label="Recode to stream" value="false" />
83 </inputs>
84 <outputs>
85 <data format="vcf" name="output" from_work_dir="out.recode.vcf">
86 </outputs>
87 <help>
88 Welcome to VCFtools - a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics. More information at http://vcftools.sourceforge.net/index.html.
89 </help>
90