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comparison snpSift_caseControl.xml @ 3:20c7d583fec1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:32 -0400
parents bf8c1526871b
children 09d6806c609e
comparison
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2:bf8c1526871b 3:20c7d583fec1
1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.1"> 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>
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 @CONDA_SNPSIFT_JAR_PATH@ && 13 SnpSift -Xmx1G caseControl -q
14 java -Xmx1G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" caseControl -q 14 #if $name.strip():
15 #if str($name).strip() != '': 15 -name '$name'
16 -name "$name" 16 #end if
17 #end if 17 #if $ctrl.ctrl_src == 'caseString':
18 #if $ctrl.ctrl_src == 'caseString': 18 '$ctrl.caseControlStr'
19 '$ctrl.caseControlStr' 19 #else
20 #else 20 -tfam '$ctrl.tfam'
21 -tfam "$ctrl.tfam" 21 #end if
22 #end if 22 '$input' > '$output'
23 "$input" > "$output" 23 ]]></command>
24 ]]>
25 </command>
26 <inputs> 24 <inputs>
27 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> 25 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
28 <conditional name="ctrl"> 26 <conditional name="ctrl">
29 <param name="ctrl_src" type="select" label="Case Control defined in"> 27 <param name="ctrl_src" type="select" label="Case Control defined in">
30 <option value="caseString">Case Control String</option> 28 <option value="caseString">Case Control String</option>
31 <option value="tfam">TFAM file</option> 29 <option value="tfam">TFAM file</option>
32 </param>
33 <when value="caseString">
34 <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
35 <help>
36 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
37 </help>
38 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
39 </param> 30 </param>
40 </when> 31 <when value="caseString">
41 <when value="tfam"> 32 <param name="caseControlStr" type="text" size="50" label="Case / Control column designation">
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"/> 33 <help>
43 </when> 34 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
35 </help>
36 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
37 </param>
38 </when>
39 <when value="tfam">
40 <param name="tfam" type="data" format="tabular" label="PLINK TFAM file" help="Read more about TFAM at http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#tr"/>
41 </when>
44 </conditional> 42 </conditional>
45 <param name="name" type="text" label="name" help="name to append to the 'Cases' or 'Controls' tags"> 43 <param name="name" type="text" label="Name" help="Name to append to the 'Cases' or 'Controls' tags">
46 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]*</validator> 44 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]*</validator>
47 </param> 45 </param>
48 </inputs> 46 </inputs>
49 <outputs> 47 <outputs>
50 <data format="vcf" name="output" /> 48 <data name="output" format="vcf" />
51 </outputs> 49 </outputs>
52 <tests> 50 <tests>
53 <test> 51 <test>
54 <param name="input" ftype="vcf" value="test.private.01.vcf"/> 52 <param name="input" ftype="vcf" value="test.private.01.vcf"/>
55 <param name="ctrl_src" value="caseString"/> 53 <param name="ctrl_src" value="caseString"/>
86 </assert_contents> 84 </assert_contents>
87 </output> 85 </output>
88 </test> 86 </test>
89 </tests> 87 </tests>
90 <help><![CDATA[ 88 <help><![CDATA[
91
92 **SnpSift CaseControl** 89 **SnpSift CaseControl**
93 90
94 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.
95 92
96 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.
97 94
98 This command adds two annotations to the VCF file: 95 This command adds two annotations to the VCF file:
99 96
100 - **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::
101 98
102 "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.*
103 100
104 101
105 - **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::
106 103
107 "CaseControl=4,0;CaseControlP=3.030303e-02" *in this case the pValue of having 4 or more cases and zero controls is 0.03* 104 "CaseControl=4,0;CaseControlP=3.030303e-02" *in this case the pValue of having 4 or more cases and zero controls is 0.03*
108
109 105
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: 106 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:
111 107
112 - Hom/Het case = "hom" 108 - Hom/Het case = "hom"
113 109 - Hom/Het control = "any"
114 - Hom/Het control = "any" 110 - Case / Control column designation = ""++++------"
115
116 - Case / Control column designation = ""++++------"
117
118 111
119 @EXTERNAL_DOCUMENTATION@ 112 @EXTERNAL_DOCUMENTATION@
120 http://snpeff.sourceforge.net/SnpSift.html#casecontrol 113 - http://snpeff.sourceforge.net/SnpSift.html#casecontrol
121 114 ]]></help>
122 ]]>
123 </help>
124 <expand macro="citations" /> 115 <expand macro="citations" />
125 </tool> 116 </tool>