|
12
|
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 <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>
|
|
|
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="none">None</option>
|
|
|
80 <option value="removeindels"> Remove indels</option>
|
|
|
81 </param>
|
|
|
82 <param name="removefilterall" type="boolean" truevalue="--remove-filtered-all" falsevalue="" label="Remove all sites with the FILTER tag" value="false" />
|
|
|
83 <param name="recodetostream" type="boolean" truevalue="--recode-to-stream" falsevalue="" label="Recode to stream" value="false" />
|
|
|
84 </inputs>
|
|
|
85 <outputs>
|
|
|
86 <data format="vcf" name="output" from_work_dir="out.recode.vcf" />
|
|
|
87 </outputs>
|
|
|
88 <help>
|
|
|
89 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.
|
|
|
90 </help>
|
|
|
91 </tool> |
