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comparison snpSift_caseControl.xml @ 8:13b6ad2ddace

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SnpEffect v3.2
author Jim Johnson <jj@umn.edu>
date Mon, 13 May 2013 12:45:07 -0500
parents ec16dae84230
children 937367efb1da
comparison
equal deleted inserted replaced
7:b26a1aff7f81 8:13b6ad2ddace
1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.1"> 1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.2">
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 will need to change the path to wherever your installation is. 4 You will need to change the path to wherever your installation is.
5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) 5 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
6 --> 6 -->
7 <requirements> 7 <requirements>
8 <requirement type="package" version="3.1">snpEff</requirement> 8 <requirement type="package" version="3.2">snpEff</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar caseControl -q $hhCase $hhControl '$caseControStr' $input > $output 11 java -Xmx1G -jar \$JAVA_JAR_PATH/SnpSift.jar caseControl -q
12 </command> 12 #if $name.__str__.strip() != '':
13 <inputs> 13 -name $name
14 <param format="vcf" name="input" type="data" label="VCF input"/> 14 #end if
15 <param name="hhCase" type="select" label="Hom/Het case"> 15 #if $ctrl.ctrl_src == 'caseString':
16 <option value="any">Any</option> 16 '$ctrl.caseControlStr'
17 <option value="hom">Homozygous</option> 17 #else
18 <option value="het">Heterozygous</option> 18 -tfam "$ctrl.tfam"
19 </param> 19 #end if
20 <param name="hhControl" type="select" label="Hom/Het control"> 20 $input > $output
21 <option value="any">Any</option> 21 </command>
22 <option value="hom">Homozygous</option> 22 <inputs>
23 <option value="het">Heterozygous</option> 23 <param format="vcf" name="input" type="data" label="VCF input"/>
24 </param> 24 <conditional name="ctrl">
25 <param name="caseControStr" type="text" label="Case / Control column designation" size="50"> 25 <param name="ctrl_src" type="select" label="Case Control defined in">
26 <help> 26 <option value="caseString">Case Control String</option>
27 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral 27 <option value="tfam">TFAM</option>
28 </help> 28 </param>
29 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator> 29 <when value="caseString">
30 </param> 30 <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
31 </inputs> 31 <help>
32 <outputs> 32 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
33 <data format="vcf" name="output" /> 33 </help>
34 </outputs> 34 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
35 </param>
36 </when>
37 <when value="tfam">
38 <param format="tabular" name="tfam" type="data" label="PLINK TFAM file"/>
39 </when>
40 </conditional>
41 <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags">
42 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator>
43 </param>
44 </inputs>
45 <outputs>
46 <data format="vcf" name="output" />
47 </outputs>
35 <stdio> 48 <stdio>
36 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 49 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
37 <exit_code range="1:" level="fatal" description="Error" /> 50 <exit_code range="1:" level="fatal" description="Error" />
38 </stdio> 51 </stdio>
39 <tests> 52 <tests>
40 53
41 <test> 54 <test>
42 <param name="input" ftype="vcf" value="test.private.01.vcf"/> 55 <param name="input" ftype="vcf" value="test.private.01.vcf"/>
43 <param name="hhCase" value="any"/> 56 <param name="ctrl_src" value="caseString"/>
44 <param name="hhControl" value="any"/> 57 <param name="caseControlStr" value="--"/>
45 <param name="caseControStr" value="--"/>
46 <output name="output"> 58 <output name="output">
47 <assert_contents> 59 <assert_contents>
48 <has_text text="CaseControl=0/0,0/2;" /> 60 <has_text text="Cases=0,0,0;" />
61 <has_text text="Controls=0,0,0;" />
49 </assert_contents> 62 </assert_contents>
50 </output> 63 </output>
51 </test> 64 </test>
52 65
53 <test> 66 <test>
54 <param name="input" ftype="vcf" value="test.private.02.vcf"/> 67 <param name="input" ftype="vcf" value="test.private.02.vcf"/>
55 <param name="hhCase" value="any"/> 68 <param name="ctrl_src" value="caseString"/>
56 <param name="hhControl" value="any"/> 69 <param name="caseControlStr" value="--"/>
57 <param name="caseControStr" value="--"/>
58 <output name="output"> 70 <output name="output">
59 <assert_contents> 71 <assert_contents>
60 <has_text text="CaseControl=0/0,2/0;" /> 72 <has_text text="Cases=0,0,0;" />
73 <has_text text="Controls=2,0,4;" />
61 </assert_contents> 74 </assert_contents>
62 </output> 75 </output>
63 </test> 76 </test>
64 77
65 <test> 78 <test>
66 <param name="input" ftype="vcf" value="test.private.02.vcf"/> 79 <param name="input" ftype="vcf" value="test.private.02.vcf"/>
67 <param name="hhCase" value="any"/> 80 <param name="name" value=""/>
68 <param name="hhControl" value="any"/> 81 <param name="ctrl_src" value="caseString"/>
69 <param name="caseControStr" value="-+"/> 82 <param name="caseControlStr" value="-+"/>
70 <output name="output"> 83 <output name="output">
71 <assert_contents> 84 <assert_contents>
72 <has_text text="CaseControl=1/0,1/0;" /> 85 <has_text text="Cases=1,0,2;" />
86 <has_text text="Controls=1,0,2;" />
73 </assert_contents> 87 </assert_contents>
74 </output> 88 </output>
75 </test> 89 </test>
76 90
77 </tests> 91 </tests>
78 92
79 <help> 93 <help>
80 94
81 **SnpSift CaseControl** 95 **SnpSift CaseControl**
82 96
83 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. 97 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants.
84 98
105 - Case / Control column designation = ""++++------" 119 - Case / Control column designation = ""++++------"
106 120
107 121
108 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol 122 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol
109 123
110 </help> 124 </help>
111 </tool> 125 </tool>