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1 <toold id="vcftools" name="VCFtools" version="0.0.1">
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2 <description>
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3 The vcftools program is intended for analysis of diploid SNP data in VCF format.
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="0.1.11">vcftools</requirement>
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7 </requirements>
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8 <command>
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9 vcftools
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10
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11 #if str($basic) == "gzvcf"
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12 --gzvcf
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13 #elif str($basic) == "bcf"
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14 --bcf
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15 #else
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16 --vcf
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17 #end if
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18
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19 $input
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20
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21 #for $chromosome in $chr
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22 --chr $chromosome.number
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23 #end for
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24
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25 #for $chromosome in $notchr
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26 --notchr $chromosome.number
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27 #end for
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28
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29 #if str($frombp) != ""
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30 --from-bp $frombp
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31 #end if
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32
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33 #if str($tobp) != ""
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34 --to-bp $tobp
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35 #end if
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36
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37 #for $snp in $snps
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38 --snp $snp.id
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39 #end for
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40
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41 #if str(${snpfile.file_name}) != ""
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42 --snps $snpfile
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43 #end if
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44
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45 #if str(${excludesnpfile.file_name}) != ""
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46 --snps $excludesnpfile
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47 #end if
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48
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49 #if str($indels) == "keeponlyindels"
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50 --keep-only-indels
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51 #elif str($indels) == "removeindels"
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52 --removeindels
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53 #end if
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54
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55 $removefilterall $recodetostream > out.recode.vcf
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56 </command>
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57 <inputs>
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58 <param name="input" type="data" label="Input vcf file" format="vcf" />
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59 <param name="basic" type="select" label="Basic Options" value="vcf">
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60 <option value="vcf">Decompressed vcf file (default)</option>
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61 <option value="gzvcf">Compressed (gzipped) vcf file</option>
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62 <option value="bcf">Compressed (bgzf) bcf file</option
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63 </param>
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64 <repeat name="chr" title="Include chromosomes to be processed">
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65 <param name="number" label="Chromosome number" type="integer" optional="true" />
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66 </repeat>
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67 <repeat name="notchr" title="Exclude chromosomes from processing">
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68 <param name="number" label="Chromosome number" type="integer" optional="true" />
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69 </repeat>
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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"/>
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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."/>
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72 <repeat name="snps" title="SNPs to include">
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73 <param name="id" label="ID of SNP" type="text" optional="true" help="e.g. a dbSNP rsID"/>
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74 </repeat>t
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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"/>
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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"/>
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77 <param name="indels" type="select" label="Indel options" value="none">
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78 <option value="keeponlyindels">Keep only indels</option>
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79 <option value="removeindels"> Remove indels</option>
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80 </param>
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81 <param name="removefilterall" type="boolean" truevalue="--remove-filtered-all" falsevalue="" label="Remove all sites with the FILTER tag" value="false" />
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82 <param name="recodetostream" type="boolean" truevalue="--recode-to-stream" falsevalue="" label="Recode to stream" value="false" />
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83 </inputs>
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84 <outputs>
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85 <data format="vcf" name="output" from_work_dir="out.recode.vcf">
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86 </outputs>
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87 <help>
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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.
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89 </help>
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90
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