view snpeff_3_3/snpSift_int.xml @ 0:80e2dbf1b1f5 draft

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<tool id="snpSift_int" name="SnpSift Intervals" version="3.3">
    <description>Filter variants using intervals </description>
    <!-- 
        You will need to change the path to wherever your installation is.
        You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
    -->
    <requirements>
                <requirement type="package" version="3.3">snpEff</requirement>
    </requirements>
    <command>
        java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="VCF input"/>
        <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
        <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals" 
                       help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
    </inputs>
    <outputs>
        <data format="vcf" name="output" />
    </outputs>
        <stdio>
          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
          <exit_code range="1:"  level="fatal"   description="Error" />
        </stdio>
        <tests>

            <test>
                <param name="input" ftype="vcf" value="annotate_5.vcf"/>
                <param name="bedFile" ftype="bed" value="interval.bed"/>
                <param name="exclude" value="False"/>
                <output name="output">
                    <assert_contents>
                        <has_text text="872687" />
                        <not_has_text text="1195966" />
                    </assert_contents>
                </output>
            </test>

            <test>
                <param name="input" ftype="vcf" value="annotate_5.vcf"/>
                <param name="bedFile" ftype="bed" value="interval.bed"/>
                <param name="exclude" value="True"/>
                <output name="output">
                    <assert_contents>
                        <has_text text="1195966" />
                        <not_has_text text="872687" />
                    </assert_contents>
                </output>
            </test>

        </tests>

    <help>

You can filter using intervals (BED file)

For details about this tool, read the fine manual_ http://snpeff.sourceforge.net/SnpSift.html#intervals

For details about this tool, please see the snpEff_ web site.

.. _snpEff: http://snpEff.sourceforge.net
.. _manual: http://snpeff.sourceforge.net/SnpSift.html#intervals
.. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
    </help>
</tool>