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comparison snpSift_int.xml @ 0:9e8280e19338 draft

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author iuc
date Thu, 22 Jan 2015 08:39:07 -0500
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1 <tool id="snpSift_int" name="SnpSift Intervals" version="4.0.0">
2 <description>Filter variants using intervals</description>
3 <!--
4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5 -->
6 <expand macro="requirements" />
7 <macros>
8 <import>snpSift_macros.xml</import>
9 </macros>
10 <command>
11 java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
12 </command>
13 <inputs>
14 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
15 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/>
16 <param name="exclude" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Exclude Intervals"
17 help="Filter out (exclude) VCF entries that match any interval in the BED files"/>
18 </inputs>
19 <outputs>
20 <data format="vcf" name="output" />
21 </outputs>
22 <expand macro="stdio" />
23 <tests>
24 <test>
25 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
26 <param name="bedFile" ftype="bed" value="interval.bed"/>
27 <param name="exclude" value="False"/>
28 <output name="output">
29 <assert_contents>
30 <has_text text="872687" />
31 <not_has_text text="1195966" />
32 </assert_contents>
33 </output>
34 </test>
35 <test>
36 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
37 <param name="bedFile" ftype="bed" value="interval.bed"/>
38 <param name="exclude" value="True"/>
39 <output name="output">
40 <assert_contents>
41 <has_text text="1195966" />
42 <not_has_text text="872687" />
43 </assert_contents>
44 </output>
45 </test>
46 </tests>
47 <help>
48
49 You can filter using intervals (BED file).
50
51 @EXTERNAL_DOCUMENTATION@
52 http://snpeff.sourceforge.net/SnpSift.html#intervals
53
54 @CITATION_SECTION@
55
56 </help>
57 </tool>