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comparison snpSift_caseControl.xml @ 14:80da7fae14b8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:10:54 -0500
parents ed810da439cc
children 8bd645802765
comparison
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13:ed810da439cc 14:80da7fae14b8
1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.0"> 1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.1">
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 <expand macro="version_command" /> 11 <expand macro="version_command" />
12 <command><![CDATA[ 12 <command><![CDATA[
13 java -Xmx1G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" caseControl -q 13 @CONDA_SNPSIFT_JAR_PATH@ &&
14 #if str($name).strip() != '': 14 java -Xmx1G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" caseControl -q
15 -name "$name" 15 #if str($name).strip() != '':
16 #end if 16 -name "$name"
17 #if $ctrl.ctrl_src == 'caseString': 17 #end if
18 '$ctrl.caseControlStr' 18 #if $ctrl.ctrl_src == 'caseString':
19 #else 19 '$ctrl.caseControlStr'
20 -tfam "$ctrl.tfam" 20 #else
21 #end if 21 -tfam "$ctrl.tfam"
22 "$input" > "$output" 22 #end if
23 "$input" > "$output"
23 ]]> 24 ]]>
24 </command> 25 </command>
25 <inputs> 26 <inputs>
26 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 27 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
27 <conditional name="ctrl"> 28 <conditional name="ctrl">
39 </when> 40 </when>
40 <when value="tfam"> 41 <when value="tfam">
41 <param format="tabular" name="tfam" type="data" label="PLINK TFAM file" help="Read more about TFAM at http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr"/> 42 <param format="tabular" name="tfam" type="data" label="PLINK TFAM file" help="Read more about TFAM at http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr"/>
42 </when> 43 </when>
43 </conditional> 44 </conditional>
44 <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags"> 45 <param name="name" type="text" label="name" help="name to append to the 'Cases' or 'Controls' tags">
45 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator> 46 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]*</validator>
46 </param> 47 </param>
47 </inputs> 48 </inputs>
48 <outputs> 49 <outputs>
49 <data format="vcf" name="output" /> 50 <data format="vcf" name="output" />
50 </outputs> 51 </outputs>
88 </tests> 89 </tests>
89 <help><![CDATA[ 90 <help><![CDATA[
90 91
91 **SnpSift CaseControl** 92 **SnpSift CaseControl**
92 93
93 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. 94 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
94 95
95 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. 96 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral.
96 97
97 This command adds two annotations to the VCF file: 98 This command adds two annotations to the VCF file:
98 99
99 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: 100 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example:
100 101
101 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.* 102 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.*
102 103
103 104
104 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example: 105 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example:
108 109
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: 110 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:
110 111
111 - Hom/Het case = "hom" 112 - Hom/Het case = "hom"
112 113
113 - Hom/Het control = "any" 114 - Hom/Het control = "any"
114 115
115 - Case / Control column designation = ""++++------" 116 - Case / Control column designation = ""++++------"
116 117
117 118
118 @EXTERNAL_DOCUMENTATION@ 119 @EXTERNAL_DOCUMENTATION@