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comparison snpSift_caseControl.xml @ 7:0ad9733e22a4

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author bgruening
date Fri, 29 Nov 2013 09:27:22 -0500
parents 8952990fcab9
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6:eb394dd65c98 7:0ad9733e22a4
1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.4"> 1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="3.4">
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 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) 5 -->
6 --> 6 <expand macro="requirements" />
7 <requirements> 7 <macros>
8 <requirement type="package" version="3.4">snpEff</requirement> 8 <import>snpEff_macros.xml</import>
9 </requirements> 9 </macros>
10 <command> 10 <command>
11 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q 11 java -Xmx1G -jar \$SNPEFF_JAR_PATH/SnpSift.jar caseControl -q
12 #if $name.__str__.strip() != '': 12 #if $name.__str__.strip() != '':
13 -name $name 13 -name $name
14 #end if 14 #end if
15 #if $ctrl.ctrl_src == 'caseString': 15 #if $ctrl.ctrl_src == 'caseString':
16 '$ctrl.caseControlStr' 16 '$ctrl.caseControlStr'
17 #else 17 #else
18 -tfam "$ctrl.tfam" 18 -tfam "$ctrl.tfam"
19 #end if 19 #end if
20 $input > $output 20 $input > $output
21 </command> 21 </command>
22 <inputs> 22 <inputs>
23 <param format="vcf" name="input" type="data" label="VCF input"/> 23 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
24 <conditional name="ctrl"> 24 <conditional name="ctrl">
25 <param name="ctrl_src" type="select" label="Case Control defined in"> 25 <param name="ctrl_src" type="select" label="Case Control defined in">
26 <option value="caseString">Case Control String</option> 26 <option value="caseString">Case Control String</option>
27 <option value="tfam">TFAM</option> 27 <option value="tfam">TFAM file</option>
28 </param>
29 <when value="caseString">
30 <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
31 <help>
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 </help>
34 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
35 </param> 28 </param>
36 </when> 29 <when value="caseString">
37 <when value="tfam"> 30 <param name="caseControlStr" type="text" label="Case / Control column designation" size="50">
38 <param format="tabular" name="tfam" type="data" label="PLINK TFAM file"/> 31 <help>
39 </when> 32 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral
40 </conditional> 33 </help>
41 <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags"> 34 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator>
42 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator> 35 </param>
43 </param> 36 </when>
44 </inputs> 37 <when value="tfam">
45 <outputs> 38 <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"/>
46 <data format="vcf" name="output" /> 39 </when>
47 </outputs> 40 </conditional>
48 <stdio> 41 <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags">
49 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> 42 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator>
50 <exit_code range="1:" level="fatal" description="Error" /> 43 </param>
51 </stdio> 44 </inputs>
52 <tests> 45 <outputs>
46 <data format="vcf" name="output" />
47 </outputs>
48 <expand macro="stdio" />
49 <tests>
50 <test>
51 <param name="input" ftype="vcf" value="test.private.01.vcf"/>
52 <param name="ctrl_src" value="caseString"/>
53 <param name="caseControlStr" value="--"/>
54 <output name="output">
55 <assert_contents>
56 <has_text text="Cases=0,0,0;" />
57 <has_text text="Controls=0,0,0;" />
58 </assert_contents>
59 </output>
60 </test>
53 61
54 <test> 62 <test>
55 <param name="input" ftype="vcf" value="test.private.01.vcf"/> 63 <param name="input" ftype="vcf" value="test.private.02.vcf"/>
56 <param name="ctrl_src" value="caseString"/> 64 <param name="ctrl_src" value="caseString"/>
57 <param name="caseControlStr" value="--"/> 65 <param name="caseControlStr" value="--"/>
58 <output name="output"> 66 <output name="output">
59 <assert_contents> 67 <assert_contents>
60 <has_text text="Cases=0,0,0;" /> 68 <has_text text="Cases=0,0,0;" />
61 <has_text text="Controls=0,0,0;" /> 69 <has_text text="Controls=2,0,4;" />
62 </assert_contents> 70 </assert_contents>
63 </output> 71 </output>
64 </test> 72 </test>
65 73
66 <test> 74 <test>
67 <param name="input" ftype="vcf" value="test.private.02.vcf"/> 75 <param name="input" ftype="vcf" value="test.private.02.vcf"/>
68 <param name="ctrl_src" value="caseString"/> 76 <param name="name" value=""/>
69 <param name="caseControlStr" value="--"/> 77 <param name="ctrl_src" value="caseString"/>
70 <output name="output"> 78 <param name="caseControlStr" value="-+"/>
71 <assert_contents> 79 <output name="output">
72 <has_text text="Cases=0,0,0;" /> 80 <assert_contents>
73 <has_text text="Controls=2,0,4;" /> 81 <has_text text="Cases=1,0,2;" />
74 </assert_contents> 82 <has_text text="Controls=1,0,2;" />
75 </output> 83 </assert_contents>
76 </test> 84 </output>
77 85 </test>
78 <test> 86 </tests>
79 <param name="input" ftype="vcf" value="test.private.02.vcf"/> 87 <help>
80 <param name="name" value=""/>
81 <param name="ctrl_src" value="caseString"/>
82 <param name="caseControlStr" value="-+"/>
83 <output name="output">
84 <assert_contents>
85 <has_text text="Cases=1,0,2;" />
86 <has_text text="Controls=1,0,2;" />
87 </assert_contents>
88 </output>
89 </test>
90
91 </tests>
92
93 <help>
94 88
95 **SnpSift CaseControl** 89 **SnpSift CaseControl**
96 90
97 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.
98 92
117 - Hom/Het control = "any" 111 - Hom/Het control = "any"
118 112
119 - Case / Control column designation = ""++++------" 113 - Case / Control column designation = ""++++------"
120 114
121 115
122 For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol 116 @EXTERNAL_DOCUMENTATION@
123 117
124 SnpEff citation: 118 @CITATION_SECTION@
125 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
126
127 SnpSift citation:
128 "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
129
130
131 119
132 </help> 120 </help>
133 </tool> 121 </tool>