view snpEff_download.xml @ 13:4be8e0068bc3

Update loc data to separate version 4 databases

<tool id="snpEff_download" name="SnpEff Download" version="4.0.0">
    <description>Download a new database</description>
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <command>
    #if $snpDb.genomeSrc == "named":
      #set genomeVersion = $snpDb.genome_version
      #set data_dir = $snpeff_db_named.extra_files_path
    ## echo $snpDb.genome_version > $snpeff_db_named; 
    ## 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 
    #else
      #set genomeVersion = $snpDb.genome_databases.fields.value
      #set data_dir = $snpeff_db_cached.extra_files_path
    ## echo $snpeff_db_cached.extra_files_path > $snpeff_db_cached; 
    ## 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 
    #end if
    ## echo $genomeVersion > $snpeff_db; 
    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $data_dir -v $genomeVersion > $logfile 
    </command>
    <inputs>
        <conditional name="snpDb">
            <param name="genomeSrc" type="select" label="Genome List">
                <option value="named">By Name</option>
                <option value="cached">Select from list</option>
            </param>
            <when value="named">
                <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
                <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
                <validator type="regex" message="A genome version name is required">\S+</validator>
                </param>
            </when>
            <when value="cached">
                <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
                    <options from_data_table="snpeff_databases">
                        <filter type="sort_by" column="0" />
                    </options>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="logfile" />
        <data format="snpeffdb" name="snpeff_db_named" label="${tool.name} ${snpDb.genome_version}" >
            <filter>snpDb['genomeSrc'] == "named"</filter>
        </data>
        <data format="snpeffdb" name="snpeff_db_cached" label="${tool.name} ${snpDb.genome_databases.fields.value}">
            <filter>snpDb['genomeSrc'] == "cached"</filter>
        </data>
    </outputs>
    <expand macro="stdio" />
    <help>

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

    </help>
</tool>