view snpSift_rmInfo.xml @ 8:5fab4f81391d draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit df8a21df77acffe40c0bc0fe0409ca1b529cd7fc"

<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.galaxy0">
    <description>remove INFO field annotations</description>
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
SnpSift -Xmx2G rmInfo
'$input'
#echo ' '.join($info_fields.split(','))
> '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
        <param name="info_fields" type="text" value="" label="Info fields to remove, e.g. EFF">
          <help>Separate multiple INFO fields with a comma, e.g.: EFF,DP</help>
          <validator type="empty_field" />
        </param>
    </inputs>
    <outputs>
        <data name="output" format="vcf" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="vcf" value="test_rmInfo.vcf"/>
            <param name="info_fields" value="EFF"/>
            <output name="output">
                <assert_contents>
                    <has_text text="DP=29" />
                    <not_has_text text="EFF=EXON" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This command removes INFO fields from a VCF file (i.e. removes annotations)

Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later.

SnpEff & SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate.
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>