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1 <tool id="bcftools_@EXECUTABLE@" name="bcftools @EXECUTABLE@" version="0.1.19.0">
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2 <description>Convert, filter, subset VCF/BCF files</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <expand macro="stdio" />
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6 <macros>
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7 <token name="@EXECUTABLE@">bcftools</token>
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8 <import>bcftools_macros.xml</import>
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9 </macros>
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10 <command>
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11 @EXECUTABLE@ view
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12 $A
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13 $varsitesonly
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14 $snpcalling
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15 ##$F
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16 $G
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17 $N
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18 $e
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19 $g
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20
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21 #if str( $output_format ) == "bcf":
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22 -b
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23 #end if
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24
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25 -D $seq_dict
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26
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27 -i $ratio
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28 -t $rate
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29
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30 $input
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31 > $output
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32
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33 </command>
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34 <inputs>
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35 <param name="input" type="data" format="bcf,vcf" label="Choose a bcf file to view" />
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36 <param name="output_format" type="select" label="Choose the output format" help="-b">
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37 <option value="vcf" selected="true">VCF</option>
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38 <option value="bcf">BCF</option>
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39 </param>
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40
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41 <param name="seq_dict" type="data" format="tabular" optional="True" label="List of chromosome names for conversion" help="(-D)" />
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42
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43 <param name="ratio" type="float" label="Use alternate INDEL-to-SNP mutation rate" value="-1" help="defaults to 0.15 (-i)" />
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44 <param name="rate" type="float" label="Mutation rate for variant calling" value="0.001" help="default to 0.001 (-t)" />
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45
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46 <param name="A" type="boolean" truevalue="-A" falsevalue="" checked="False"
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47 label="Retain all possible alternate alleles at variant sites" help="-A" />
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48 <param name="varsitesonly" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Output Potential Variant Sites Only" help="-v"/>
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49 <param name="snpcalling" type="boolean" truevalue="-c" falsevalue="" checked="false" label="SNP calling" help="Forces -e the max-likelihood inference parameter. (-c)"/>
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50 <!--param name="F" type="boolean" truevalue="-F" falsevalue="" checked="False"
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51 label="Indicate PL is generated by r921 or before (ordering is different)" help="-F" /-->
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52 <param name="G" type="boolean" truevalue="-G" falsevalue="" checked="False"
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53 label="Suppress all individual genotype information" help="-G" />
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54 <param name="N" type="boolean" truevalue="-N" falsevalue="" checked="False"
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55 label="Skip sites where the REF field is not A/C/G/T" help="-N" />
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56 <param name="e" type="boolean" truevalue="-e" falsevalue="" checked="False"
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57 label="Perform max-likelihood inference only"
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58 help="Including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT. (-e)" />
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59 <param name="g" type="boolean" truevalue="-g" falsevalue="" checked="True"
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60 label="Call per-sample genotypes at variant sites" help="-g" />
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61 </inputs>
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62
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63 <outputs>
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64 <data format="bcf" name="output">
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65 <change_format>
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66 <when input="output_format" value="vcf" format="vcf" />
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67 </change_format>
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68 </data>
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69 </outputs>
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70
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71 <tests>
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72 </tests>
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73
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74 <help>
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75 <![CDATA[
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76 **BCFTools View**
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77
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78 VCF/BCF conversion, view, subset and filter VCF/BCF files.
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79
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80
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81 **Input format**
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82
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83 `BCF files <http://www.1000genomes.org/wiki/analysis/variant-call-format/bcf-binary-vcf-version-2/>`_
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84
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85 ------
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86
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87 **Outputs**
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88
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89 VCF or BCF files
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90
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91 ]]>
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92 </help>
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93 <expand macro="citations"/>
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94 </tool>
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