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comparison vcf2maf.xml @ 0:2973994fecd6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit 30046d5e0df4d80ac687edd03cf44b2afaa04550
author iuc
date Tue, 28 Jun 2022 21:07:04 +0000
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children e8510e04a86a
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-1:000000000000 0:2973994fecd6
1 <tool id="vcf2maf" name="Convert VCF to MAF" version="@TOOL_VERSION@">
2 <description>with vcf2maf</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.6.21</token>
5 <token name="@DB_VERSION@">106</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">vcf2maf</requirement>
9 <requirement type="package" version="@DB_VERSION@.1">ensembl-vep</requirement>
10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[
12 ln -s '${input1}' MainInput.vcf &&
13 #if $ref_seq.ref_source == "cached":
14 ln -s '${ref_seq.ref.fields.path}' reference.fa &&
15 #elif $ref_seq.ref_source == "history":
16 ln -s '${ref_seq.ref}' reference.fa &&
17 #end if
18 vcf2maf.pl --input-vcf MainInput.vcf --output-maf MainOutput.maf --ref-fasta reference.fa
19 #if $annotation_cache.source == "no_vep":
20 --inhibit-vep
21 #else:
22 --vep-path \$(dirname \$(which vep))
23 --vep-data '${annotation_cache.cache_file.fields.path}'
24 --species '${annotation_cache.cache_file.fields.species}'
25 --ncbi-build '${annotation_cache.cache_file.fields.value.split($annotation_cache.cache_file.fields.version + "_")[-1]}'
26 #if $annotation_cache.cache_file.fields.version != "@DB_VERSION@": --cache-version $annotation_cache.cache_file.fields.version
27 #end if
28
29 #if $tumor_id:
30 --tumor-id '${tumor_id}'
31 #end if
32 #if $normal_id:
33 --normal-id '${normal_id}'
34 #end if
35 #if $vcf_tumor_id:
36 --vcf-tumor-id '${vcf_tumor_id}'
37 #end if
38 #if $vcf_normal_id:
39 --vcf-normal-id '${vcf_normal_id}'
40 #end if
41
42 #if $adv_opt.any_allele:
43 --any-allele
44 #end if
45 #if $adv_opt.min_hom_vaf:
46 --min-hom-vaf $adv_opt.min_hom_vaf
47 #end if
48 #if $adv_opt.maf_center:
49 --maf-center '${adv_opt.maf_center}'
50 #end if
51 #if $adv_opt.retain_info:
52 --retain-info '${adv_opt.retain_info}'
53 #end if
54 #if $adv_opt.retain_fmt:
55 --retain-fmt '${adv_opt.retain_fmt}'
56 #end if
57 #if $adv_opt.retain_ann:
58 --retain-ann '${adv_opt.retain_ann}'
59 #end if
60 ]]></command>
61 <inputs>
62 <param type="data" name="input1" label="VCF input file" format="vcf">
63 <validator type="unspecified_build" />
64 </param>
65 <conditional name="ref_seq">
66 <param name="ref_source" type="select" label="Select FASTA file as reference sequence">
67 <option value="cached">Locally cached</option>
68 <option value="history">History</option>
69 </param>
70 <when value="cached">
71 <param name="ref" type="select" label="Select reference sequence">
72 <options from_data_table="fasta_indexes">
73 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
74 </options>
75 </param>
76 </when>
77 <when value="history">
78 <param name="ref" type="data" format="fasta" label="Select reference sequence" />
79 </when>
80 </conditional>
81 <conditional name="annotation_cache">
82 <param name="source" type="select" label="Select the source of annotation data if you want to use VEP" help="vcf2maf can utilize Ensembl's VEP to select a single effect per variant. VEP can only be used if SIFT is available for the selected genome assembly. Ensembl strongly recommends to only use annotation cache files with a version number matching the VEP version. You can disable the corresponding filtering of available cache files at your own risk.">
83 <option value="no_vep" selected="true">Do not use VEP</option>
84 <option value="restricted">Use VEP with a cache file with matching version number</option>
85 <option value="unrestricted">Use VEP with any cache file</option>
86 </param>
87 <when value="no_vep"/>
88 <when value="restricted">
89 <param name="cache_file" type="select" label="Select annotation cache file" help="If the annotation data of interest is not listed, have a look at all available cache files regardless of their version number or contact your Galaxy admin.">
90 <options from_data_table="vep_versioned_annotation_cache">
91 <filter type="static_value" value="@DB_VERSION@" column="2" />
92 <filter type="sort_by" column="4"/>
93 </options>
94 <validator type="no_options" message="No annotation caches are available"/>
95 </param>
96 </when>
97 <when value="unrestricted">
98 <param name="cache_file" type="select" label="Select annotation cache file" help="If the annotation data of interest is not listed, contact your Galaxy admin.">
99 <options from_data_table="vep_versioned_annotation_cache">
100 <filter type="sort_by" column="4"/>
101 </options>
102 <validator type="no_options" message="No annotation caches are available"/>
103 </param>
104 </when>
105 </conditional>
106
107 <param argument="--tumor-id" type="text" optional="true" label="Enter tumor sample ID (optional)" help="Used to fill the Tumor_Sample_Barcode column of the output MAF with the tumor sample ID."/>
108 <param argument="--normal-id" type="text" optional="true" label="Enter normal sample ID (optional)" help="Used to fill the Matched_Norm_Sample_Barcode column of the output MAF with the normal sample ID."/>
109 <param argument="--vcf-tumor-id" type="text" optional="true" label="Enter name of tumor genotype column (optional)" help="VCFs from variant callers like VarScan use hardcoded sample IDs TUMOR/NORMAL to name genotype columns. Use this parameter to have vcf2maf correctly locate these columns to parse genotypes, while still printing proper sample IDs in the output MAF."/>
110 <param argument="--vcf-normal-id" type="text" optional="true" label="Enter name of normal genotype column (optional)" help="VCFs from variant callers like VarScan use hardcoded sample IDs TUMOR/NORMAL to name genotype columns. Use this parameter to have vcf2maf correctly locate these columns to parse genotypes, while still printing proper sample IDs in the output MAF."/>
111
112 <section name="adv_opt" title="Advanced options">
113 <param argument="--any-allele" type="boolean" optional="true" checked="false" label="Allow also mismatched variant alleles when reporting co-located variants"/>
114 <param argument="--min-hom-vaf" type="float" optional="true" min="0" max="1" label="Enter minimum allele fraction to call a variant homozygous if GT is undefined in VCF" help="Default value is 0.7"/>
115 <param argument="--maf-center" type="text" optional="true" label="Enter variant calling center to report in MAF"/>
116 <param argument="--retain-info" type="text" optional="true" label="Enter comma-delimited names of INFO fields to retain as extra columns in MAF"/>
117 <param argument="--retain-fmt" type="text" optional="true" label="Enter comma-delimited names of FORMAT fields to retain as extra columns in MAF"/>
118 <param argument="--retain-ann" type="text" optional="true" label="Enter comma-delimited names of VEP annotations (within the VEP CSQ/ANN) to retain as extra columns in MAF"/>
119 </section>
120 </inputs>
121 <outputs>
122 <data name="output1" format="tabular" from_work_dir="MainOutput.maf" />
123 </outputs>
124 <tests>
125 <test expect_num_outputs="1">
126 <param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
127 <param name="ref_source" value="history" />
128 <param name="ref" dbkey="hg19" value="test1.fa" ftype="fasta" />
129 <param name="annotation_cache.source" value="no_vep" />
130 <output name="output1" file="output_test1.tabular" ftype="tabular" />
131 </test>
132 <test expect_num_outputs="1">
133 <param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
134 <param name="ref_source" value="cached" />
135 <param name="ref" value="hg19test" />
136 <param name="annotation_cache.source" value="no_vep" />
137 <output name="output1" file="output_test1.tabular" ftype="tabular" />
138 </test>
139 <test expect_num_outputs="1">
140 <param name="input1" dbkey="dm6" value="input_test2.vcf" ftype="vcf" />
141 <param name="ref_source" value="history" />
142 <param name="ref" dbkey="dm6" value="test2.fa" ftype="fasta" />
143 <param name="source" value="restricted" />
144 <param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
145 <output name="output1" file="output_test2.tabular" ftype="tabular" />
146 </test>
147 </tests>
148 <help><![CDATA[
149 The tool vcf2maf can parse a wide range of VCF-like formats and convert these into the `Mutation Annotation Format (MAF) <https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/>`__. A central part of the conversion process is the selection of a single effect per variant. While this is often a subjective decision, vcf2maf offers a standardized way to achieve this by optionally utilizing Ensembl's `Variant Effect Predictor (VEP) <https://www.ensembl.org/info/docs/tools/vep/index.html>`__. ]]></help>
150 <citations>
151 <citation type="doi">10.5281/zenodo.593251</citation>
152 </citations>
153 </tool>