Mercurial > repos > iuc > snpsift

comparison snpSift_caseControl.xml @ 11:b884686a80dc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
author iuc
date Mon, 04 May 2015 22:37:06 -0400
parents f0faaa4d6ee5
children 6bf58286d795
comparison
equal deleted inserted replaced
10:93577c5e76ec 11:b884686a80dc
1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="4.0.0"> 1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="4.0.0">
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 <expand macro="requirements" />
7 <macros> 6 <macros>
8 <import>snpSift_macros.xml</import> 7 <import>snpSift_macros.xml</import>
9 </macros> 8 </macros>
9 <expand macro="requirements" />
10 <expand macro="stdio" />
10 <command> 11 <command>
11 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 12 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q
12 #if $name.__str__.strip() != '': 13 #if $name.__str__.strip() != '':
13 -name $name 14 -name $name
14 #end if 15 #end if
15 #if $ctrl.ctrl_src == 'caseString': 16 #if $ctrl.ctrl_src == 'caseString':
16 '$ctrl.caseControlStr' 17 '$ctrl.caseControlStr'
17 #else 18 #else
18 -tfam "$ctrl.tfam" 19 -tfam "$ctrl.tfam"
19 #end if 20 #end if
20 $input > $output 21 $input > $output
21 </command> 22 </command>
43 </param> 44 </param>
44 </inputs> 45 </inputs>
45 <outputs> 46 <outputs>
46 <data format="vcf" name="output" /> 47 <data format="vcf" name="output" />
47 </outputs> 48 </outputs>
48 <expand macro="stdio" />
49 <tests> 49 <tests>
50 <test> 50 <test>
51 <param name="input" ftype="vcf" value="test.private.01.vcf"/> 51 <param name="input" ftype="vcf" value="test.private.01.vcf"/>
52 <param name="ctrl_src" value="caseString"/> 52 <param name="ctrl_src" value="caseString"/>
53 <param name="caseControlStr" value="--"/> 53 <param name="caseControlStr" value="--"/>
86 </tests> 86 </tests>
87 <help> 87 <help>
88 88
89 **SnpSift CaseControl** 89 **SnpSift CaseControl**
90 90
91 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. 91 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
92 92
93 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. 93 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral.
94 94
95 This command adds two annotations to the VCF file: 95 This command adds two annotations to the VCF file:
96 96
97 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: 97 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example:
98 98
99 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.* 99 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.*
100 100
101 101
102 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example: 102 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example:
106 106
107 For example, if we have ten samples (which means ten genotype columns in the VCF file), the first four are 'case' and the last six are 'control', so the description string would be "++++------". Let's say we want to distinguish genotypes that are homozygous in 'case' and either homozygous or heterozygous in 'control'. We would set: 107 For example, if we have ten samples (which means ten genotype columns in the VCF file), the first four are 'case' and the last six are 'control', so the description string would be "++++------". Let's say we want to distinguish genotypes that are homozygous in 'case' and either homozygous or heterozygous in 'control'. We would set:
108 108
109 - Hom/Het case = "hom" 109 - Hom/Het case = "hom"
110 110
111 - Hom/Het control = "any" 111 - Hom/Het control = "any"
112 112
113 - Case / Control column designation = ""++++------" 113 - Case / Control column designation = ""++++------"
114 114
115 115
116 @EXTERNAL_DOCUMENTATION@ 116 @EXTERNAL_DOCUMENTATION@