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comparison snpSift_filter.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 192a236898f5
children 937367efb1da
comparison
equal deleted inserted replaced
7:b26a1aff7f81 8:13b6ad2ddace
1 <tool id="snpSift_filter" name="SnpSift Filter" version="3.1"> 1 <tool id="snpSift_filter" name="SnpSift Filter" version="3.2">
2 <options sanitize="False" /> 2 <options sanitize="False" />
3 <description>Filter variants using arbitrary expressions</description> 3 <description>Filter variants using arbitrary expressions</description>
4 <!--
5 You will need to change the path to wherever your installation is.
6 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
7 java -Xmx6G -jar $JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output
8 -->
9 <requirements> 4 <requirements>
10 <requirement type="package" version="3.1">snpEff</requirement> 5 <requirement type="package" version="3.2">snpEff</requirement>
11 </requirements> 6 </requirements>
12 <command> 7 <command>
13 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile > $output 8 java -Xmx6G -jar \$JAVA_JAR_PATH/SnpSift.jar filter -f $input -e $exprFile $inverse $pass
9 #if $filterId and len($filterId.__str__.strip()) > 0:
10 --filterId = "$filterId"
11 #end if
12 #if $addFilter and len($addFilter.__str__.strip()) > 0:
13 --addFilter = "$addFilter"
14 #end if
15 #if $rmFilter and len($rmFilter.__str__.strip()) > 0:
16 --rmFilter = "$rmFilter"
17 #end if
18 > $output
14 </command> 19 </command>
15 <inputs> 20 <inputs>
16 <param format="vcf" name="input" type="data" label="VCF input"/> 21 <param format="vcf" name="input" type="data" label="VCF input"/>
17 <param name="expr" type="text" label="Expression" size="50"/> 22 <param name="expr" type="text" label="Expression" size="120"/>
23 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse. Show lines that do not match filter expression"/>
24 <param name="pass" type="boolean" truevalue="--pass" falsevalue="" checked="false" label="Use 'PASS' field instead of filtering out VCF entries"/>
25 <param name="filterId" type="text" value="" optional="true" label="ID for this filter (##FILTER tag in header and FILTER VCF field)." size="10"/>
26 <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." size="10"/>
27 <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." size="10"/>
18 </inputs> 28 </inputs>
19 <configfiles> 29 <configfiles>
20 <configfile name="exprFile"> 30 <configfile name="exprFile">
21 $expr 31 $expr
22 </configfile> 32 </configfile>
35 <test> 45 <test>
36 <param name="input" ftype="vcf" value="test01.vcf"/> 46 <param name="input" ftype="vcf" value="test01.vcf"/>
37 <param name="expr" value="QUAL >= 50"/> 47 <param name="expr" value="QUAL >= 50"/>
38 <output name="output"> 48 <output name="output">
39 <assert_contents> 49 <assert_contents>
40 <not_has_text text="25967" /> 50 <has_text text="28837706" />
41 <not_has_text text="NT_166464" /> 51 <not_has_text text="NT_166464" />
42 </assert_contents> 52 </assert_contents>
43 </output> 53 </output>
44 </test> 54 </test>
45 55
54 </output> 64 </output>
55 </test> 65 </test>
56 66
57 <test> 67 <test>
58 <param name="input" ftype="vcf" value="test01.vcf"/> 68 <param name="input" ftype="vcf" value="test01.vcf"/>
59 <param name="expr" value="(POS >= 20175 & (POS <= 35549)"/> 69 <param name="expr" value="(POS >= 20175) &amp; (POS &lt;= 35549)"/>
60 <output name="output"> 70 <output name="output">
61 <assert_contents> 71 <assert_contents>
62 <has_text text="20175" /> 72 <has_text text="20175" />
63 <has_text text="35549" /> 73 <has_text text="35549" />
64 <has_text text="22256" /> 74 <has_text text="22256" />