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1 <tool id="maf2maf" name="maf2maf" version="1.0.0">
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2 <description>Reannotates MAF file creating a new MAF file</description>
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3
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4 <command>
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5 echo \$VCF2MAF_SCRIPT_PATH;
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6 echo \$ENSEMBL_VEP_84_INSTALL_DIR;
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7 cat $input_maf | perl -ne '@a=split /\t/;if(\$a[4] == 23){\$a[4] = "X";}print join "\t", @a;' > ./input.maf;
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8 perl \$VCF2MAF_SCRIPT_PATH/maf2maf.pl
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9 --input-maf ./input.maf
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10 --output-maf $output_maf
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11 --vep-path \$ENSEMBL_VEP_84_INSTALL_DIR
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12 --vep-data \${ENSEMBL_VEP_84_INSTALL_DIR}/cache
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13 --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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14 --species `echo $species_select.value | sed 's/-/\t/g' | cut -f1`
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15 --ncbi-build `echo $species_select.value | sed 's/-/\t/g' | cut -f2`;
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16 </command>
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17
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18 <inputs>
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19 <expand macro="genome_list" />
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20 <param name="input_maf" type="data" format="maf" label="Input MAF file" />
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21 </inputs>
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22
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23 <outputs>
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24 <data name="output_maf" format="maf" label="#echo os.path.splitext( str( $input_maf.name ) )[ 0 ] #.${tool.name}.maf" />
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25 </outputs>
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26
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27 <stdio>
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28 <exit_code range="1:" level="fatal" description="Failure" />
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29 </stdio>
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30
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31 <requirements>
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3
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32 <requirement type="package" version="5.18.1">perl</requirement>
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33 <requirement type="package" version="1.6.7">vcf2maf</requirement>
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34 <requirement type="package" version="84">ensembl_vep_perl_env</requirement>
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35 <requirement type="package" version="84">ensembl_vep</requirement>
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36 <requirement type="package" version="1.6.7">vcf2maf</requirement>
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37 <requirement type="paclage" version="84">ensembl_vep_perl_environment</requirement>
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38 </requirements>
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39
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40 <macros>
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41 <import>ensembl_vep_macros.xml</import>
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42 </macros>
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43
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44 <help>
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45
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46 </help>
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47
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48 </tool>
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