comparison snpSift_int.xml @ 3:20c7d583fec1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5

2:bf8c1526871b

<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.1">
    <description>Filter variants using intervals</description>
    <!-- 
        You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
    -->
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @CONDA_SNPSIFT_JAR_PATH@ &&
        java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" intervals -i "$input" $exclude "$bedFile" > "$output"
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <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>
    <tests>
        <test>
            <param name="input" ftype="vcf" value="annotate_5.vcf"/>
            <param name="bedFile" ftype="bed" value="interval.bed"/>

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

You can filter using intervals (BED file).

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

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

3:20c7d583fec1

<tool id="snpSift_int" name="SnpSift Intervals" version="@WRAPPER_VERSION@.0">
    <description>Filter variants using intervals</description>
    <!--
        You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
    -->
    <macros>
        <import>snpSift_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
SnpSift -Xmx2G intervals
-i '$input'
$exclude
'$bedFile'
> '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
        <param name="bedFile" type="data" format="bed" 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 name="output" format="vcf" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="vcf" value="annotate_5.vcf"/>
            <param name="bedFile" ftype="bed" value="interval.bed"/>

                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
You can filter using intervals (BED file).

@EXTERNAL_DOCUMENTATION@
- http://snpeff.sourceforge.net/SnpSift.html#intervals
    ]]></help>
    <expand macro="citations" />
</tool>