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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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14 </requirements>
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15 <command><![CDATA[
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16 #if str($veptools.veptoolsselect) =="downloadcache"
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17
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18 cd \$CONDA_DEFAULT_ENV && [[ -d vep_cache ]] || mkdir vep_cache ;
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19 cd bin && perl vep_install.pl
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20 -a ac -s $veptools.species
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21 --NO_HTSLIB
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22 --CACHEDIR \$CONDA_DEFAULT_ENV/vep_cache;
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23 ## write the cache file downloaded
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24 echo "CACHE DOWNLOADED YET">$output1;
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25 ls \$CONDA_DEFAULT_ENV/vep_cache/*/ >> $output1;
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26 #end if
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27
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28
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29 #if str($veptools.veptoolsselect) =="annotate"
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30 perl \$CONDA_DEFAULT_ENV/bin/variant_effect_predictor.pl
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31 --fork \${GALAXY_SLOTS:-4}
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32 --offline
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33 --dir \$CONDA_DEFAULT_ENV/vep_cache
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34 --force_overwrite
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35 #if $veptools.everything.value
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36 --everything
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37 #end if
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38 --species $veptools.species
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39 --buffer_size $veptools.buffer
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40 --vcf
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41 --input_file $veptools.input
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42 --output_file $output2
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43 --stats_file stat.htm
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44 #end if
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45
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46
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47 #if str($veptools.veptoolsselect) =="vcf2maf"
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48 ln -s $veptools.input_vcf ./input.vcf;
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49 perl $__tool_directory__/vcf2maf.pl
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50 --input-vcf ./input.vcf
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51 --output-maf $output_maf
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52 --vep-forks 1
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53 --tumor-id $veptools.tumour_id
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54 --normal-id $veptools.normal_id
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55 --buffer-size $veptools.buffer
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56 --vep-path \$CONDA_DEFAULT_ENV/bin/
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57 --vep-data \$CONDA_DEFAULT_ENV/vep_cache
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58 --ref-fasta $veptools.reference
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59 --species $veptools.species;
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60
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61 #end if
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62 ]]>
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63 </command>
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64 <inputs>
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65 <conditional name="veptools">
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66 <param name="veptoolsselect" type="select" label="vep">
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67 <option value="downloadcache" selected="true">vep-download-cache</option>
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68 <option value="annotate">vep-annotate</option>
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69 <option value="vcf2maf">vcf2maf</option>
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70 </param>
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71 <when value="downloadcache">
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72 <expand macro="list-cache"/>
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73 </when>
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74 <when value="annotate">
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75 <expand macro="vep-annotate-inputs-macro"/>
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76 <expand macro="list-cache-annotate"/>
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77 </when>
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78 <when value="vcf2maf">
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79 <expand macro="vcf2maf-inputs-macro"/>
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80 <expand macro="list-vcf2maf"/>
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81 </when>
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82 </conditional>
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83 </inputs>
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84 <outputs>
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85 <!--vep-download-cache-outputs-->
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86 <data format="txt" name="output1" label="cache downloaded">
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87 <filter>veptools['veptoolsselect'] == 'downloadcache'</filter>
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88 </data>
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89 <!--vep-annotate-outputs-->
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90 <data format="vcf" name="output2" label="vep-annotated on ${on_string} ">
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91 <filter>veptools['veptoolsselect'] == 'annotate'</filter>
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92 </data>
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93 <data format="html" name="stat" from_work_dir="stat.htm" label="stat on ${on_string}">
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94 <filter>veptools['veptoolsselect'] == 'annotate'</filter>
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95 </data>
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96 <!--vcf2maf-outputs-->
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97 <data name="output_maf" format="maf" label="vcf2maf on ${on_string} ">
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98 <filter>veptools['veptoolsselect'] == 'vcf2maf'</filter>
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99 </data>
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100 </outputs>
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101 <stdio>
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102 <exit_code range="1:" level="fatal" description="Failure" />
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103 </stdio>
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104 <citations>
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105 <citation type="doi">10.1186/s13059-016-0974-4</citation>
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106 </citations>
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107 <help>
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108 **IMPORTANT**
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109 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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110
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111 **what it does**
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112
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113 - **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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114
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115 - **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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116
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117 - **vcf2maf** convert vcf in MAF format calling vep_annotate.
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118
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119 </help>
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120 </tool>
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