comparison snpSift_rmInfo.xml @ 8:2f40467536cf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 93465571cf180554c3548338a68fa0f1604985dc-dirty

7:c29f29a6f26c

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
      java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar rmInfo $input ' '.join($info_fields.split(',')) > $output
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param name="info_fields" type="text" value="" label="Info fields to remove, e.g. EFF">

The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry  in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones. 

@EXTERNAL_DOCUMENTATION@
    http://snpeff.sourceforge.net/SnpSift.html#rmInfo

@CITATION_SECTION@

]]>
    </help>
</tool>

8:2f40467536cf

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
      java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" rmInfo "$input" ' '.join($info_fields.split(',')) > "$output"
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param name="info_fields" type="text" value="" label="Info fields to remove, e.g. EFF">

The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry  in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones. 

@EXTERNAL_DOCUMENTATION@
    http://snpeff.sourceforge.net/SnpSift.html#rmInfo

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