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author nilesh
date Wed, 10 Jul 2013 17:46:09 -0400
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1 <tool 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 <command>
6 vcftools
7
8 #if str($basic) == "gzvcf"
9 --gzvcf
10 #elif str($basic) == "bcf"
11 --bcf
12 #else
13 --vcf
14 #end if
15
16 $input
17
18 #for $chromosome in $chr
19 --chr $chromosome.number
20 #end for
21
22 #for $chromosome in $notchr
23 --notchr $chromosome.number
24 #end for
25
26 #if str($frombp) != ""
27 --from-bp $frombp
28 #end if
29
30 #if str($tobp) != ""
31 --to-bp $tobp
32 #end if
33
34 #for $snp in $snps
35 --snp $snp.id
36 #end for
37
38 #if str(${snpfile.file_name}) != ""
39 --snps $snpfile
40 #end if
41
42 #if str(${excludesnpfile.file_name}) != ""
43 --snps $excludesnpfile
44 #end if
45
46 #if str($indels) == "keeponlyindels"
47 --keep-only-indels
48 #elif str($indels) == "removeindels"
49 --removeindels
50 #end if
51
52 $removefilterall $recodetostream > out.recode.vcf
53 </command>
54 <inputs>
55 <param name="input" type="data" label="Input vcf file" format="vcf" />
56 <param name="basic" type="select" label="Basic Options" value="vcf">
57 <option value="vcf">Decompressed vcf file (default)</option>
58 <option value="gzvcf">Compressed (gzipped) vcf file</option>
59 <option value="bcf">Compressed (bgzf) bcf file</option>
60 </param>
61 <repeat name="chr" title="Include chromosomes to be processed">
62 <param name="number" label="Chromosome number" type="integer" optional="true" />
63 </repeat>
64 <repeat name="notchr" title="Exclude chromosomes from processing">
65 <param name="number" label="Chromosome number" type="integer" optional="true" />
66 </repeat>
67 <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"/>
68 <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."/>
69 <repeat name="snps" title="SNPs to include">
70 <param name="id" label="ID of SNP" type="text" optional="true" help="e.g. a dbSNP rsID"/>
71 </repeat>
72 <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"/>
73 <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"/>
74 <param name="indels" type="select" label="Indel options" value="none">
75 <option value="keeponlyindels">Keep only indels</option>
76 <option value="none">None</option>
77 <option value="removeindels"> Remove indels</option>
78 </param>
79 <param name="removefilterall" type="boolean" truevalue="--remove-filtered-all" falsevalue="" label="Remove all sites with the FILTER tag" value="false" />
80 <param name="recodetostream" type="boolean" truevalue="--recode-to-stream" falsevalue="" label="Recode to stream" value="false" />
81 </inputs>
82 <outputs>
83 <data format="vcf" name="output" from_work_dir="out.recode.vcf" />
84 </outputs>
85 <help>
86 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.
87 </help>
88 </tool>