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1 <tool id="vep-unico" name="vep-unico" version="1.0.0">
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2 <description>
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3 wrapper for variant-effect-predictor86 and vcf2maf
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4 </description>
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5 <macros>
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6 <import>vep-unico-macros.xml</import>
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7 <import>vcf2maf-macros.xml</import>
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8 <import>vep-download-cache-macros.xml</import>
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9 <import>vep-annotate-macros.xml</import>
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10 </macros>
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11 <requirements>
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12 <requirement type="package" version="86">variant-effect-predictor</requirement>
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13 <requirement type="package" version="1.3.1">samtools</requirement>
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3
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14 <requirement type="package" version="1.0" >openssl</requirement>
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4
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15 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
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16 </requirements>
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17 <command><![CDATA[
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18 #if str($veptools.veptoolsselect) =="downloadcache"
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19
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3
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20 cd \$CONDA_PREFIX && [[ -d vep_cache ]] || mkdir vep_cache ;
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21 cd bin && perl vep_install.pl
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22 -a ac -s $veptools.species
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23 --NO_HTSLIB
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24 --CACHEDIR \$CONDA_PREFIX/vep_cache;
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25 ## write the cache file downloaded
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26 echo "CACHE DOWNLOADED YET">$output1;
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27 ls \$CONDA_PREFIX/vep_cache/*/ >> $output1;
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28 #end if
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29
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30
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31 #if str($veptools.veptoolsselect) =="annotate"
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32 perl \$CONDA_PREFIX/bin/variant_effect_predictor.pl
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2
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33 --fork 4
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34 --offline
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35 --dir \$CONDA_PREFIX/vep_cache
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36 --force_overwrite
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37 #if $veptools.everything.value
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38 --everything
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39 #end if
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40 --species $veptools.species
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41 --buffer_size $veptools.buffer
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42 --vcf
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43 --input_file $veptools.input
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44 --output_file $output2
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45 --stats_file stat.htm
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46 #end if
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47
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48
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49 #if str($veptools.veptoolsselect) =="vcf2maf"
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50 ln -s $veptools.input_vcf ./input.vcf;
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51 perl $__tool_directory__/vcf2maf.pl
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52 --input-vcf ./input.vcf
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53 --output-maf $output_maf
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54 --vep-forks 1
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55 --tumor-id $veptools.tumour_id
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56 --normal-id $veptools.normal_id
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57 --buffer-size $veptools.buffer
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3
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58 --vep-path \$CONDA_PREFIX/bin/
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59 --vep-data \$CONDA_PREFIX/vep_cache
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60
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61
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62
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63
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64
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65 #if $veptools.reference_source.reference_source_selector == "history"
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66 --ref-fasta $veptools.reference_source.reference
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67 #end if
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68 #if $veptools.reference_source.reference_source_selector == "cached"
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69 --ref-fasta $veptools.reference_source.ref_file.fields.path
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70 #end if
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71
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72 --species $veptools.species
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73 --filter-vcf 0 ;
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74
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75 #end if
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76 ]]>
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77 </command>
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78 <inputs>
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79 <conditional name="veptools">
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80 <param name="veptoolsselect" type="select" label="vep">
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81 <option value="downloadcache" selected="true">vep-download-cache</option>
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82 <option value="annotate">vep-annotate</option>
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83 <option value="vcf2maf">vcf2maf</option>
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84 </param>
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85 <when value="downloadcache">
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86 <expand macro="list-cache"/>
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87 </when>
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88 <when value="annotate">
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89 <expand macro="vep-annotate-inputs-macro"/>
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90 <expand macro="list-cache-annotate"/>
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91 </when>
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92 <when value="vcf2maf">
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93 <expand macro="vcf2maf-inputs-macro"/>
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94 <expand macro="list-vcf2maf"/>
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95 </when>
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96 </conditional>
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97 </inputs>
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98 <outputs>
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99 <!--vep-download-cache-outputs-->
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100 <data format="txt" name="output1" label="cache downloaded">
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101 <filter>veptools['veptoolsselect'] == 'downloadcache'</filter>
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102 </data>
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103 <!--vep-annotate-outputs-->
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104 <data format="vcf" name="output2" label="vep-annotated on ${on_string} ">
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105 <filter>veptools['veptoolsselect'] == 'annotate'</filter>
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106 </data>
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107 <data format="html" name="stat" from_work_dir="stat.htm" label="stat on ${on_string}">
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108 <filter>veptools['veptoolsselect'] == 'annotate'</filter>
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109 </data>
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110 <!--vcf2maf-outputs-->
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111 <data name="output_maf" format="maf" label="vcf2maf on ${on_string} ">
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112 <filter>veptools['veptoolsselect'] == 'vcf2maf'</filter>
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113 </data>
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114 </outputs>
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115 <stdio>
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116 <exit_code range="1:" level="fatal" description="Failure" />
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117 </stdio>
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118 <citations>
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119 <citation type="doi">10.1186/s13059-016-0974-4</citation>
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120 </citations>
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121 <help>
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122 **IMPORTANT**
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123 before running vep_annotate or vcf2maf tool for the first time you have to download the cache file using vep_download_cache
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124
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125 **what it does**
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126
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127 - **vep_annotate** determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
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128
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129 - **vep_download_cache** download the cache file, used by vep v.86.It is a file containing all transcript models, regulatory features and variant data for a species.
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130
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131 - **vcf2maf** convert vcf in MAF format calling vep_annotate.
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132
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133 </help>
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134 </tool>
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