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comparison snpSift_int.xml @ 8:13b6ad2ddace

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SnpEffect v3.2
author Jim Johnson <jj@umn.edu>
date Mon, 13 May 2013 12:45:07 -0500
parents ec16dae84230
children 937367efb1da
comparison
equal deleted inserted replaced
7:b26a1aff7f81 8:13b6ad2ddace
1 <tool id="snpSift_int" name="SnpSift Intervals" version="3.1"> 1 <tool id="snpSift_int" name="SnpSift Intervals" version="3.2">
2 <description>Filter variants using intervals </description> 2 <description>Filter variants using intervals </description>
3 <!-- 3 <!--
4 You will need to change the path to wherever your installation is. 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) 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="package" version="3.1">snpEff</requirement> 8 <requirement type="package" version="3.2">snpEff</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 cat $input | java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar int $bedFile > $output 11 java -Xmx2G -jar \$JAVA_JAR_PATH/SnpSift.jar intervals -i $input $exclude $bedFile > $output
12 </command> 12 </command>
13 <inputs> 13 <inputs>
14 <param format="vcf" name="input" type="data" label="VCF input"/> 14 <param format="vcf" name="input" type="data" label="VCF input"/>
15 <param format="bed" name="bedFile" type="data" label="Intervals (BED file)"/> 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"/>
16 </inputs> 18 </inputs>
17 <outputs> 19 <outputs>
18 <data format="vcf" name="output" /> 20 <data format="vcf" name="output" />
19 </outputs> 21 </outputs>
20 <stdio> 22 <stdio>
21 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 23 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
22 <exit_code range="1:" level="fatal" description="Error" /> 24 <exit_code range="1:" level="fatal" description="Error" />
23 </stdio> 25 </stdio>
24 <tests> 26 <tests>
27
25 <test> 28 <test>
26 <param name="input" ftype="vcf" value="annotate_5.vcf"/> 29 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
27 <param name="bedFile" ftype="bed" value="interval.bed"/> 30 <param name="bedFile" ftype="bed" value="interval.bed"/>
31 <param name="exclude" value="False"/>
28 <output name="output"> 32 <output name="output">
29 <assert_contents> 33 <assert_contents>
30 <has_text text="872687" /> 34 <has_text text="872687" />
31 <not_has_text text="1195966" /> 35 <not_has_text text="1195966" />
36 </assert_contents>
37 </output>
38 </test>
39
40 <test>
41 <param name="input" ftype="vcf" value="annotate_5.vcf"/>
42 <param name="bedFile" ftype="bed" value="interval.bed"/>
43 <param name="exclude" value="True"/>
44 <output name="output">
45 <assert_contents>
46 <has_text text="1195966" />
47 <not_has_text text="872687" />
32 </assert_contents> 48 </assert_contents>
33 </output> 49 </output>
34 </test> 50 </test>
35 51
36 </tests> 52 </tests>