comparison snpEff_download.xml @ 1:500832f27cbc draft

Uploaded

0:e8adfc4c0a6b

<tool id="snpEff_download" name="SnpEff Download" version="3.4">
    <description>Download a new database</description>
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <command>
    echo $genomeVersion > $snpeff_db; 
    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.extra_files_path -v $genomeVersion > $logfile 
    </command>
    <inputs>
        <param name="genomeVersion" type="select" label="Select the genome version you want to download">
            <options from_data_table="snpeff_databases">
                <filter type="sort_by" column="0" />
            </options>
        </param>
    </inputs>
    <outputs>
        <data format="txt" name="logfile" />
        <data format="snpeffdb" name="snpeff_db" label="${genomeVersion}" />
    </outputs>
    <expand macro="stdio" />
    <help>

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

    </help>
</tool>

1:500832f27cbc

<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0">
    <description>Download a new database</description>
    <expand macro="requirements" />
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <command>
<![CDATA[
    java -jar \$SNPEFF_JAR_PATH/snpEff.jar download -c \$SNPEFF_JAR_PATH/snpEff.config -dataDir $snpeff_db.files_path -v $genome_version 
]]>
    </command>
    <inputs>
        <param name="genome_version" type="text" size="40" value="" label="Select the genome version you want to download (e.g. GRCh37.74)">
            <help>@SNPEFF_DATABASE_URL@</help>
            <validator type="regex" message="A genome version name is required">\S+</validator>
        </param>
    </inputs>
    <outputs>
        <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" />
    </outputs>
    <expand macro="stdio" />
    <help>

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

    </help>
    <expand macro="citations" />
</tool>