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1 <tool id="vcf2maf" name="vcf2maf" version="1.0.0">
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2 <description>Converts VCF files into MAF format</description>
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3
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4 <command>
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6
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5 echo \$(which perl)
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6 echo \$VCF2MAF_SCRIPT_PATH;
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7 echo \$ENSEMBL_VEP_84_INSTALL_DIR;
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8 ln -s $input_vcf ./input.vcf;
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9 perl \$VCF2MAF_SCRIPT_PATH/vcf2maf.pl
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10 --input-vcf ./input.vcf
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11 --output-maf $output_maf
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9
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12 --vep-forks 1
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13 #if $sampleid_source.sampleid_selector == "bamfile":
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14 --tumor-id `basename $sampleid_source.sampleid_tumour | sed 's/.bam$//g'`
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15 --normal-id `basename $sampleid_source.sampleid_normal | sed 's/.bam$//g'`
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16 #else:
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17 --tumor-id $sampleid_source.tumour_id
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18 --normal-id $sampleid_source.normal_id
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19 #end if
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20
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21 --vep-path \$ENSEMBL_VEP_84_INSTALL_DIR
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22 --vep-data \${ENSEMBL_VEP_84_INSTALL_DIR}/cache
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23 --ref-fasta \${ENSEMBL_VEP_84_INSTALL_DIR}/cache/`echo $species_select.value | sed 's/-/\t/g' | cut -f1`/84_`echo $species_select.value | sed 's/-/\t/g' | cut -f2`/*.fa
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24 --species `echo $species_select.value | sed 's/-/\t/g' | cut -f1`
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25 --ncbi-build `echo $species_select.value | sed 's/-/\t/g' | cut -f2`;
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10
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26 mv $output_maf temp.maf;
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27 grep -v version temp.maf > $output_maf;
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28 </command>
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29
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30 <inputs>
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31 <conditional name="sampleid_source">
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32 <param label="Choose the source to open the Sample Id" name="sampleid_selector" type="select">
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33 <option value="bamfile">Bam File Name</option>
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34 <option value="manual">Manual</option>
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35 </param>
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36 <when value="bamfile">
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37 <param type="data" format="bam" name="sampleid_normal" label="Normal Bam"/>
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38 <param type="data" format="bam" name="sampleid_tumour" label="Tumour Bam"/>
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39 </when>
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40 <when value="manual">
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41 <param name="tumour_id" type="text" label="Tumour ID (Name)"/>
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42 <param name="normal_id" type="text" label="Normal ID (Name)"/>
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43 </when>
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44 </conditional>
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45 <expand macro="genome_list"/>
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46 <param name="input_vcf" type="data" format="vcf" label="Input VCF File" />
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47 </inputs>
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48
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49 <outputs>
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50 <data name="output_maf" format="maf" label="#echo os.path.splitext( str( $input_vcf.name ) )[ 0 ] #.${tool.name}.maf" />
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51 </outputs>
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52
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53 <stdio>
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54 <exit_code range="1:" level="fatal" description="Failure" />
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55 </stdio>
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56
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57 <requirements>
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8
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58
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3
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59 <requirement type="package" version="5.18.1">perl</requirement>
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60 <requirement type="package" version="84">ensembl_vep</requirement>
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61 <requirement type="package" version="1.6.7">vcf2maf</requirement>
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8
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62 <requirement type="package" version="84">ensembl_vep_perl_env</requirement>
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63 </requirements>
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64
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65 <macros>
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66 <import>ensembl_vep_macros.xml</import>
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67 </macros>
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68
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69 <help>
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70
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71 </help>
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72 </tool>
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