view snpSift_macros.xml @ 6:2b3e65a4252f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 693e1a3641c776965f68d688c8e1409adba7da1e

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="4.3.1t">snpsift</requirement>
            <!--Coreutils are required to make readlink work across platforms. Previous version did not work on MacOS-->
            <requirement type="package" version="8.25">coreutils</requirement>
            <!--PERL is required to make SnpSift helper scripts run-->
            <requirement type="package" version="5.26">perl</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
            <exit_code range="1:" level="fatal" description="Error" />
        </stdio>
    </xml>
    <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token>
    <xml name="version_command">
        <version_command><![CDATA[
SnpSift dbnsfp 2>&1|head -n 1
        ]]></version_command>
    </xml>
    <token name="@WRAPPER_VERSION@">4.3+t</token>
    <token name="@EXTERNAL_DOCUMENTATION@">
For details about this tool, please go to:

- http://snpeff.sourceforge.net/SnpEff_manual.html
    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.3389/fgene.2012.00035</citation>
            <yield />
        </citations>
    </xml>
</macros>