Mercurial > repos > greg > snpeff_v2_from_pablo
diff snpEff_2_1a/galaxy/snpSift_int.xml @ 0:f8eaa3f8194b default tip
Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
| author | greg |
|---|---|
| date | Fri, 20 Apr 2012 14:47:09 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/galaxy/snpSift_int.xml Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,25 @@ +<tool id="snpSift_int" name="SnpSift Intervals" version="1.0"> + <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) + --> + <command> + cat $input | java -Xmx2G -jar /home/pcingola/tools/SnpSift.jar int $bedFile > $output + </command> + <inputs> + <param format="Tabular" name="input" type="data" label="VCF input"/> + <param format="Tabular" name="bedFile" type="data" label="Intervals (BED file)"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +You can filter using intervals (BED file) + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals + + </help> +</tool>