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annotate snpEff_download.xml @ 15:fac49d7ea7d4

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Update tool revisions to 4.0.1
author Jim Johnson <jj@umn.edu>
date Tue, 21 Oct 2014 14:40:44 -0500
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1 <tool id="snpEff_download" name="SnpEff Download" version="4.0.1">
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2 <description>Download a new database</description>
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3 <expand macro="requirements" />
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4 <macros>
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5 <import>snpEff_macros.xml</import>
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6 </macros>
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7 <command>
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8 #if $snpDb.genomeSrc == "named":
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9 #set genomeVersion = $snpDb.genome_version
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10 #set data_dir = $snpeff_db_named.extra_files_path
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11 ## echo $snpDb.genome_version > $snpeff_db_named;
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12 ## java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db_named.extra_files_path -v $snpDb.genome_version > $logfile
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13 #else
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14 #set genomeVersion = $snpDb.genome_databases.fields.value
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15 #set data_dir = $snpeff_db_cached.extra_files_path
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16 ## echo $snpeff_db_cached.extra_files_path > $snpeff_db_cached;
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17 ## java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db_cached.extra_files_path -v $snpeff_db_cached.extra_files_path > $logfile
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18 #end if
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19 ## echo $genomeVersion > $snpeff_db;
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20 java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $data_dir -v $genomeVersion > $logfile
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21 </command>
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22 <inputs>
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23 <conditional name="snpDb">
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24 <param name="genomeSrc" type="select" label="Genome List">
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25 <option value="named">By Name</option>
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26 <option value="cached">Select from list</option>
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27 </param>
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28 <when value="named">
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29 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
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30 <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
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31 <validator type="regex" message="A genome version name is required">\S+</validator>
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32 </param>
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33 </when>
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34 <when value="cached">
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35 <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
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36 <options from_data_table="snpeff4_databases">
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37 <filter type="sort_by" column="0" />
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38 </options>
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39 </param>
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40 </when>
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41 </conditional>
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42 </inputs>
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43 <outputs>
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44 <data format="txt" name="logfile" />
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45 <data format="snpeffdb" name="snpeff_db_named" label="${tool.name} ${snpDb.genome_version}" >
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46 <filter>snpDb['genomeSrc'] == "named"</filter>
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47 </data>
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48 <data format="snpeffdb" name="snpeff_db_cached" label="${tool.name} ${snpDb.genome_databases.fields.value}">
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49 <filter>snpDb['genomeSrc'] == "cached"</filter>
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50 </data>
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51 </outputs>
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52 <expand macro="stdio" />
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53 <help>
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55 @EXTERNAL_DOCUMENTATION@
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57 @CITATION_SECTION@
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59 </help>
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60 </tool>
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