comparison snpSift_annotate.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 -Xmx6G -jar \$SNPEFF_JAR_PATH/SnpSift.jar $annotate_cmd 
        #if $annotate.id :
          -id
        #elif $annotate.info_ids.__str__.strip() != '' :
          -info "$annotate.info_ids"
        #end if          
        -q $dbSnp $input > $output 
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 

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

@CITATION_SECTION@


]]>
    </help>
</tool>

8:2f40467536cf

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" $annotate_cmd 
        #if $annotate.id :
          -id
        #elif str($annotate.info_ids).strip() != '' :
          -info "$annotate.info_ids"
        #end if          
        -q "$dbSnp" "$input" > "$output" 
]]>
    </command>
    <inputs>
        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
        <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" 

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

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