Mercurial > repos > iuc > snpsift
annotate snpSift_caseControl.xml @ 7:2e497a770bca draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 200c7d062259a94a28c6a224586f59d1a5e08309"
author | iuc |
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date | Sun, 29 Nov 2020 21:14:56 +0000 |
parents | 09d6806c609e |
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09d6806c609e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
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1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.galaxy0"> |
0 | 2 <description>Count samples are in 'case' and 'control' groups.</description> |
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bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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3 <!-- |
0 | 4 You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) |
5 --> | |
6 <macros> | |
7 <import>snpSift_macros.xml</import> | |
8 </macros> | |
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98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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9 <expand macro="requirements" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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10 <expand macro="stdio" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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11 <expand macro="version_command" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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12 <command><![CDATA[ |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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13 SnpSift -Xmx1G caseControl -q |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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14 #if $name.strip(): |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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15 -name '$name' |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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16 #end if |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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17 #if $ctrl.ctrl_src == 'caseString': |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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18 '$ctrl.caseControlStr' |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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19 #else |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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20 -tfam '$ctrl.tfam' |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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21 #end if |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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22 '$input' > '$output' |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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23 ]]></command> |
0 | 24 <inputs> |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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25 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> |
0 | 26 <conditional name="ctrl"> |
27 <param name="ctrl_src" type="select" label="Case Control defined in"> | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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28 <option value="caseString">Case Control String</option> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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29 <option value="tfam">TFAM file</option> |
0 | 30 </param> |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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31 <when value="caseString"> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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32 <param name="caseControlStr" type="text" size="50" label="Case / Control column designation"> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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33 <help> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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34 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents:
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35 </help> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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36 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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37 </param> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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38 </when> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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39 <when value="tfam"> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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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"/> |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents:
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41 </when> |
0 | 42 </conditional> |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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43 <param name="name" type="text" label="Name" help="Name to append to the 'Cases' or 'Controls' tags"> |
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bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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44 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]*</validator> |
0 | 45 </param> |
46 </inputs> | |
47 <outputs> | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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48 <data name="output" format="vcf" /> |
0 | 49 </outputs> |
50 <tests> | |
51 <test> | |
52 <param name="input" ftype="vcf" value="test.private.01.vcf"/> | |
53 <param name="ctrl_src" value="caseString"/> | |
54 <param name="caseControlStr" value="--"/> | |
55 <output name="output"> | |
56 <assert_contents> | |
57 <has_text text="Cases=0,0,0;" /> | |
58 <has_text text="Controls=0,0,0;" /> | |
59 </assert_contents> | |
60 </output> | |
61 </test> | |
62 | |
63 <test> | |
64 <param name="input" ftype="vcf" value="test.private.02.vcf"/> | |
65 <param name="ctrl_src" value="caseString"/> | |
66 <param name="caseControlStr" value="--"/> | |
67 <output name="output"> | |
68 <assert_contents> | |
69 <has_text text="Cases=0,0,0;" /> | |
70 <has_text text="Controls=2,0,4;" /> | |
71 </assert_contents> | |
72 </output> | |
73 </test> | |
74 | |
75 <test> | |
76 <param name="input" ftype="vcf" value="test.private.02.vcf"/> | |
77 <param name="name" value=""/> | |
78 <param name="ctrl_src" value="caseString"/> | |
79 <param name="caseControlStr" value="-+"/> | |
80 <output name="output"> | |
81 <assert_contents> | |
82 <has_text text="Cases=1,0,2;" /> | |
83 <has_text text="Controls=1,0,2;" /> | |
84 </assert_contents> | |
85 </output> | |
86 </test> | |
87 </tests> | |
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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88 <help><![CDATA[ |
0 | 89 **SnpSift CaseControl** |
90 | |
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bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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91 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. |
0 | 92 |
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bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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93 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. |
0 | 94 |
95 This command adds two annotations to the VCF file: | |
96 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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97 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example:: |
0 | 98 |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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99 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.* |
0 | 100 |
101 | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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102 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example:: |
0 | 103 |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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* |
0 | 105 |
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: | |
107 | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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108 - Hom/Het case = "hom" |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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109 - Hom/Het control = "any" |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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110 - Case / Control column designation = ""++++------" |
0 | 111 |
112 @EXTERNAL_DOCUMENTATION@ | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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113 - http://snpeff.sourceforge.net/SnpSift.html#casecontrol |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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114 ]]></help> |
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98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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115 <expand macro="citations" /> |
0 | 116 </tool> |