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1 <tool id="annotate" name="Annotate" version="1.0.0">
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2 <description>
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3 Annotate VCF files using Ensemble VEP
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4 </description>
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5 <command>
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6 perl \$ENSEMBL_VEP_84_INSTALL_DIR/variant_effect_predictor.pl
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7 --fork 4
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8 --offline
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9 --species \$( echo $species_select.value | sed 's/#/\t/g' | cut -f1)
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10 --dir \$ENSEMBL_VEP_76_CACHE_DIR
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11 --no_stats
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12 --force_overwrite
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13 --everything
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14 --check_existing
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15 --total_length
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16 --allele_number
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17 --no_escape
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18 --gencode_basic
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19 --xref_refseq
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20 #if "#" in $species_select.value
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21 --assembly \$( echo $species_select.value | sed 's/#/\t/g' | cut -f2)
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22 #end if
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23 --vcf
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24 --input_file $input_vcf
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25 --output_file $output_vcf
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26 </command>
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27 <inputs>
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28 <param name="input_vcf" type="data" format="vcf" label="Input VCF File" />
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29 <expand macro="genome_list"/>
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30 </inputs>
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31
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32 <outputs>
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33 <data format="vcf" name="output_vcf" label="${input.name}_vep-annotated" />
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34 </outputs>
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35
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36 <stdio>
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37 <exit_code range="1:" level="fatal" description="Failure" />
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38 </stdio>
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39
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40 <requirements>
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41 <requirement type="package" version="84">ensembl_vep</requirement>
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42 <requirement type="package" version="5.18.1">perl</requirement>
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43 </requirements>
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44 <macros>
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45 <import>ensembl_vep_macros.xml</import>
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46 </macros>
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47
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48 </tool>
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