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19
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1 <tool id="download_cache" name="Get VEP Cache" version="1.0.0">
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2 <description>
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3 Download and Index Genomes and Reference files used by Ensemble VEP
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="84">ensembl_vep</requirement>
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7 </requirements>
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8 <command>
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9 #if $use_mirror.value == "no":
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10 perl \$ENSEMBL_VEP_84_INSTALL_DIR/INSTALL.pl
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11 --AUTO cf
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12 --SPECIES \$(echo $species_select.value | sed 's/-/\t/g' | cut -f1)
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13 --CACHEDIR \$ENSEMBL_VEP_84_INSTALL_DIR/cache
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14 #if "-" in $species_select.value
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15 --ASSEMBLY \$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)
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16 #end if
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17 ;
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18 #else:
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19 perl \$ENSEMBL_VEP_84_INSTALL_DIR/INSTALL.pl
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20 --AUTO cf
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21 --SPECIES \$(echo $species_select.value | sed 's/-/\t/g' | cut -f1)
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22 --CACHEDIR \$ENSEMBL_VEP_84_INSTALL_DIR/cache
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23 --CACHEURL ftp://ftp03.bcgsc.ca/public/ensembl/VEP/ --FASTAURL ftp://ftp03.bcgsc.ca/public/ensembl/
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24 #if "-" in $species_select.value
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25 --ASSEMBLY \$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)
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26 #end if
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27 ;
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28 #end if
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29 gzip -d \$ENSEMBL_VEP_84_INSTALL_DIR/cache/\$(echo $species_select.value | sed 's/-/\t/g' | cut -f1 | sed 's/\ /_/g')/*\$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)/*.fa.gz;
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30 samtools faidx \$ENSEMBL_VEP_84_INSTALL_DIR/cache/\$(echo $species_select.value | sed 's/-/\t/g' | cut -f1 | sed 's/\ /_/g')/*\$(echo $species_select.value | sed 's/-/\t/g' | cut -f2)/*.fa;
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31
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32 env > $output;
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33 </command>
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34 <inputs>
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35 <expand macro="genome_list" />
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36 <param name="use_mirror" type="boolean" checked="false" label="use North American mirror site for download" display="radio" truevalue="yes" falsevalue="no"/>
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37 </inputs>
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38 <outputs>
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39 <data format="txt" name="output"/>
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40 </outputs>
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41 <stdio>
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42 <exit_code range="1:" level="fatal" description="Failure" />
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43 </stdio>
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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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