Mercurial > repos > jjohnson > snpsift

comparison snpSift_caseControl.xml @ 4:baf6602903e1

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Wed, 09 Dec 2015 14:03:26 -0500
parents 796388c291d3
children 2f40467536cf
comparison
equal deleted inserted replaced
3:1739678def32 4:baf6602903e1
1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="4.0.0"> 1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.0">
2 <description>Count samples are in 'case' and 'control' groups.</description> 2 <description>Count samples are in 'case' and 'control' groups.</description>
3 <!-- 3 <!--
4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
5 --> 5 -->
6 <macros>
7 <import>snpSift_macros.xml</import>
8 </macros>
6 <expand macro="requirements" /> 9 <expand macro="requirements" />
7 <macros> 10 <expand macro="stdio" />
8 <import>snpEff_macros.xml</import> 11 <expand macro="version_command" />
9 </macros> 12 <command><![CDATA[
10 <command>
11 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 13 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q
12 #if $name.__str__.strip() != '': 14 #if $name.__str__.strip() != '':
13 -name $name 15 -name $name
14 #end if 16 #end if
15 #if $ctrl.ctrl_src == 'caseString': 17 #if $ctrl.ctrl_src == 'caseString':
16 '$ctrl.caseControlStr' 18 '$ctrl.caseControlStr'
17 #else 19 #else
18 -tfam "$ctrl.tfam" 20 -tfam "$ctrl.tfam"
19 #end if 21 #end if
20 $input > $output 22 $input > $output
23 ]]>
21 </command> 24 </command>
22 <inputs> 25 <inputs>
23 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 26 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
24 <conditional name="ctrl"> 27 <conditional name="ctrl">
25 <param name="ctrl_src" type="select" label="Case Control defined in"> 28 <param name="ctrl_src" type="select" label="Case Control defined in">
43 </param> 46 </param>
44 </inputs> 47 </inputs>
45 <outputs> 48 <outputs>
46 <data format="vcf" name="output" /> 49 <data format="vcf" name="output" />
47 </outputs> 50 </outputs>
48 <expand macro="stdio" />
49 <tests> 51 <tests>
50 <test> 52 <test>
51 <param name="input" ftype="vcf" value="test.private.01.vcf"/> 53 <param name="input" ftype="vcf" value="test.private.01.vcf"/>
52 <param name="ctrl_src" value="caseString"/> 54 <param name="ctrl_src" value="caseString"/>
53 <param name="caseControlStr" value="--"/> 55 <param name="caseControlStr" value="--"/>
82 <has_text text="Controls=1,0,2;" /> 84 <has_text text="Controls=1,0,2;" />
83 </assert_contents> 85 </assert_contents>
84 </output> 86 </output>
85 </test> 87 </test>
86 </tests> 88 </tests>
87 <help> 89 <help><![CDATA[
88 90
89 **SnpSift CaseControl** 91 **SnpSift CaseControl**
90 92
91 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. 93 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
92 94
116 @EXTERNAL_DOCUMENTATION@ 118 @EXTERNAL_DOCUMENTATION@
117 http://snpeff.sourceforge.net/SnpSift.html#casecontrol 119 http://snpeff.sourceforge.net/SnpSift.html#casecontrol
118 120
119 @CITATION_SECTION@ 121 @CITATION_SECTION@
120 122
123 ]]>
121 </help> 124 </help>
122 </tool> 125 </tool>