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1 <tool id="vcfs2fasta" name="VCFs to fasta" version="1.0">
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2 <description>Takes a set of VCF files and outputs a multi fasta file with only the variant positions.</description>
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3 <requirements>
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4 <requirement type="package" version="2.7.10">python</requirement>
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5 <requirement type="package" version="0.6.8dev">pyvcf</requirement>
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6 <requirement type="package" version="3.11">pyyaml</requirement>
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7 <requirement type="package" version="2.0.2">bintrees</requirement>
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8 <requirement type="package" version="1.66">biopython</requirement>
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9 <requirement type="package" version="1.4">matplotlib</requirement>
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3
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10 <requirement type="package" version="1.0">phephenix</requirement>
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0
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11 </requirements>
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12 <stdio>
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13 <!-- Assume anything other than zero is an error -->
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14 <exit_code range="1:" />
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15 <exit_code range=":-1" />
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16 </stdio>
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17 <command interpreter="bash">
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18 vcfs2fasta.sh
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19 $output
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20 #if str($mix_cond.mix) == "yes":
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21 $mix_cond.mix_value
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22 #else
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23 NOTTHERE
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24 #end if
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25 #if str($cols_cond.cols) == "yes":
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26 $cols_cond.column_ns
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27 #else
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28 NOTTHERE
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29 #end if
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30 #if str($sample_cond.sample) == "yes":
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31 $sample_cond.sample_ns
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32 #else
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33 NOTTHERE
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34 #end if
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35 #if str($reference_cond.reference) == "yes":
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36 $reference_cond.ref_fa
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37 #else
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38 NOTTHERE
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39 #end if
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40 #if str($include_cond.include) == "yes":
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41 $include_cond.in_bed
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42 #else
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43 NOTTHERE
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44 #end if
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45 #if str($exclude_cond.exclude) == "yes":
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46 $exclude_cond.ex_bed
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47 #else
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48 NOTTHERE
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49 #end if
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50 #for $i, $input_vcf in enumerate( $input_vcfs ):
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51 "${input_vcf}"
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52 #end for
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53 </command>
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54
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55 <inputs>
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56 <param name="input_vcfs" type="data" multiple="true" format="vcf" label="Input VCF file(s)" />
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57 <conditional name="mix_cond">
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58 <param name="mix" type="select" label="With Mixtures" help="Specify this option with a threshold to output mixtures above this threshold.">
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59 <option value="yes">Specify</option>
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60 <option value="no" selected="true">Do not specify</option>
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61 </param>
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62 <when value="yes">
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63 <param name="mix_value" type="float" value="0.5" label="Mixture value" />
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64 </when>
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65 </conditional>
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66 <conditional name="cols_cond">
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67 <param name="cols" type="select" label="Column Ns" help="Keeps columns with fraction of Ns above specified threshold.">
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68 <option value="yes">Specify</option>
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69 <option value="no" selected="true">Do not specify</option>
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70 </param>
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71 <when value="yes">
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72 <param name="column_ns" type="float" value="0.5" label="Column Ns value" />
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73 </when>
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74 </conditional>
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75 <conditional name="sample_cond">
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76 <param name="sample" type="select" label="Sample Ns" help="Keeps samples with fraction of Ns above specified threshold.">
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77 <option value="yes">Specify</option>
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78 <option value="no" selected="true">Do not specify</option>
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79 </param>
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80 <when value="yes">
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81 <param name="sample_ns" type="float" value="0.5" label="Sample Ns value" />
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82 </when>
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83 </conditional>
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84 <conditional name="reference_cond">
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85 <param name="reference" type="select" label="Reference genome file" help="If path to reference specified, then whole genome will be outputted.">
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86 <option value="yes">Specify</option>
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87 <option value="no" selected="true">Do not specify</option>
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88 </param>
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89 <when value="yes">
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90 <param name="ref_fa" type="data" format="fasta" label="Reference fasta file" help="Fasta format"/>
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91 </when>
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92 </conditional>
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93 <conditional name="include_cond">
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94 <param name="include" type="select" label="Include region" help="Specify regions to include in a bed file.">
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95 <option value="yes">Specify</option>
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96 <option value="no" selected="true">Do not specify</option>
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97 </param>
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98 <when value="yes">
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99 <param name="in_bed" type="data" format="bed" label="Include regions bed file" help="bed format"/>
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100 </when>
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101 </conditional>
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102 <conditional name="exclude_cond">
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103 <param name="exclude" type="select" label="Exclude region" help="Specify regions to exclude in a bed file.">
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104 <option value="yes">Specify</option>
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105 <option value="no" selected="true">Do not specify</option>
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106 </param>
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107 <when value="yes">
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108 <param name="ex_bed" type="data" format="bed" label="Exclude regions bed file" help="bed format"/>
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109 </when>
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110 </conditional>
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111 </inputs>
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112
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113 <outputs>
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114 <data format="fasta" name="output" label="${tool.name} on ${on_string}: FASTA file" />
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115 </outputs>
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116 <test>
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117 <param name="input_vcfs" value="1_short.vcf" ftype="vcf" />
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118 <param name="input_vcfs" value="2_short.vcf" ftype="vcf" />
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119 <output name="output" file="testresult.fa" ftype="fasta" />
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120 </test>
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121 <help>
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122
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123 </help>
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124 </tool>
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