|
0
|
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>
|
