Mercurial > repos > iuc > snpsift

comparison snpSift_caseControl.xml @ 13:ed810da439cc 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 d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:41:13 -0400
parents 6bf58286d795
children 80da7fae14b8
comparison
equal deleted inserted replaced
12:6bf58286d795 13:ed810da439cc
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> 6 <macros>
7 <import>snpSift_macros.xml</import> 7 <import>snpSift_macros.xml</import>
8 </macros> 8 </macros>
9 <expand macro="requirements" /> 9 <expand macro="requirements" />
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <command> 11 <expand macro="version_command" />
12 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 12 <command><![CDATA[
13 #if $name.__str__.strip() != '': 13 java -Xmx1G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" caseControl -q
14 -name $name 14 #if str($name).strip() != '':
15 -name "$name"
15 #end if 16 #end if
16 #if $ctrl.ctrl_src == 'caseString': 17 #if $ctrl.ctrl_src == 'caseString':
17 '$ctrl.caseControlStr' 18 '$ctrl.caseControlStr'
18 #else 19 #else
19 -tfam "$ctrl.tfam" 20 -tfam "$ctrl.tfam"
20 #end if 21 #end if
21 $input > $output 22 "$input" > "$output"
23 ]]>
22 </command> 24 </command>
23 <inputs> 25 <inputs>
24 <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"/>
25 <conditional name="ctrl"> 27 <conditional name="ctrl">
26 <param name="ctrl_src" type="select" label="Case Control defined in"> 28 <param name="ctrl_src" type="select" label="Case Control defined in">
27 <option value="caseString">Case Control String</option> 29 <option value="caseString">Case Control String</option>
28 <option value="tfam">TFAM file</option> 30 <option value="tfam">TFAM file</option>
29 </param> 31 </param>
30 <when value="caseString"> 32 <when value="caseString">
31 <param name="caseControlStr" type="text" label="Case / Control column designation"> 33 <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
32 <help> 34 <help>
33 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral 35 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
34 </help> 36 </help>
35 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator> 37 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
36 </param> 38 </param>
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
93 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. 95 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral.
94 96
95 This command adds two annotations to the VCF file: 97 This command adds two annotations to the VCF file:
96 98
97 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: 99 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example:
98 100
99 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.* 101 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.*
100 102
101 103
102 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example: 104 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example:
106 108
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: 109 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:
108 110
109 - Hom/Het case = "hom" 111 - Hom/Het case = "hom"
110 112
111 - Hom/Het control = "any" 113 - Hom/Het control = "any"
112 114
113 - Case / Control column designation = ""++++------" 115 - Case / Control column designation = ""++++------"
114 116
115 117
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 ]]>
120 122 </help>
121 </help> 123 <expand macro="citations" />
122 </tool> 124 </tool>