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