Mercurial > repos > jjohnson > snpeff

comparison snpSift_int.xml @ 0:c07c403fc470

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Thu, 17 Jan 2013 16:31:12 -0500
parents
children 192a236898f5
comparison
equal deleted inserted replaced
-1:000000000000 0:c07c403fc470
1 <tool id="snpSift_int" name="SnpSift Intervals" version="3.1">
2 <description>Filter variants using intervals </description>
3 <!--
4 You will need to change the path to wherever your installation is.
5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
6 -->
7 <requirements>
8 <requirement type="package" version="3.1">snpEff</requirement>
9 </requirements>
10 <command>
11 cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output
12 </command>
13 <inputs>
14 <param format="vcf" name="input" type="data" label="VCF input"/>
15 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
16 </inputs>
17 <outputs>
18 <data format="vcf" name="output" />
19 </outputs>
20 <stdio>
21 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
22 <exit_code range="1:" level="fatal" description="Error" />
23 </stdio>
24 <help>
25
26 You can filter using intervals (BED file)
27
28 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals
29
30 </help>
31 </tool>