Mercurial > repos > iuc > snpsift
annotate snpSift_caseControl.xml @ 2:bf8c1526871b draft
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 12:11:18 -0500 |
| parents | 98708b88af9f |
| children | 20c7d583fec1 |
| rev | line source |
|---|---|
|
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.1"> |
| 0 | 2 <description>Count samples are in 'case' and 'control' groups.</description> |
|
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
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> | |
|
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
0
diff
changeset
|
9 <expand macro="requirements" /> |
|
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
0
diff
changeset
|
10 <expand macro="stdio" /> |
|
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
0
diff
changeset
|
11 <expand macro="version_command" /> |
|
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
0
diff
changeset
|
12 <command><![CDATA[ |
|
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
13 @CONDA_SNPSIFT_JAR_PATH@ && |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
14 java -Xmx1G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" caseControl -q |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
15 #if str($name).strip() != '': |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
16 -name "$name" |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
17 #end if |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
18 #if $ctrl.ctrl_src == 'caseString': |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
19 '$ctrl.caseControlStr' |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
20 #else |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
21 -tfam "$ctrl.tfam" |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
22 #end if |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
23 "$input" > "$output" |
|
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
0
diff
changeset
|
24 ]]> |
| 0 | 25 </command> |
| 26 <inputs> | |
| 27 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
| 28 <conditional name="ctrl"> | |
| 29 <param name="ctrl_src" type="select" label="Case Control defined in"> | |
| 30 <option value="caseString">Case Control String</option> | |
| 31 <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> | |
| 40 </when> | |
| 41 <when value="tfam"> | |
| 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"/> | |
| 43 </when> | |
| 44 </conditional> | |
|
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
45 <param name="name" type="text" label="name" help="name to append to the 'Cases' or 'Controls' tags"> |
|
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
46 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]*</validator> |
| 0 | 47 </param> |
| 48 </inputs> | |
| 49 <outputs> | |
| 50 <data format="vcf" name="output" /> | |
| 51 </outputs> | |
| 52 <tests> | |
| 53 <test> | |
| 54 <param name="input" ftype="vcf" value="test.private.01.vcf"/> | |
| 55 <param name="ctrl_src" value="caseString"/> | |
| 56 <param name="caseControlStr" value="--"/> | |
| 57 <output name="output"> | |
| 58 <assert_contents> | |
| 59 <has_text text="Cases=0,0,0;" /> | |
| 60 <has_text text="Controls=0,0,0;" /> | |
| 61 </assert_contents> | |
| 62 </output> | |
| 63 </test> | |
| 64 | |
| 65 <test> | |
| 66 <param name="input" ftype="vcf" value="test.private.02.vcf"/> | |
| 67 <param name="ctrl_src" value="caseString"/> | |
| 68 <param name="caseControlStr" value="--"/> | |
| 69 <output name="output"> | |
| 70 <assert_contents> | |
| 71 <has_text text="Cases=0,0,0;" /> | |
| 72 <has_text text="Controls=2,0,4;" /> | |
| 73 </assert_contents> | |
| 74 </output> | |
| 75 </test> | |
| 76 | |
| 77 <test> | |
| 78 <param name="input" ftype="vcf" value="test.private.02.vcf"/> | |
| 79 <param name="name" value=""/> | |
| 80 <param name="ctrl_src" value="caseString"/> | |
| 81 <param name="caseControlStr" value="-+"/> | |
| 82 <output name="output"> | |
| 83 <assert_contents> | |
| 84 <has_text text="Cases=1,0,2;" /> | |
| 85 <has_text text="Controls=1,0,2;" /> | |
| 86 </assert_contents> | |
| 87 </output> | |
| 88 </test> | |
| 89 </tests> | |
|
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
0
diff
changeset
|
90 <help><![CDATA[ |
| 0 | 91 |
| 92 **SnpSift CaseControl** | |
| 93 | |
|
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
94 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. |
| 0 | 95 |
|
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
96 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. |
| 0 | 97 |
| 98 This command adds two annotations to the VCF file: | |
| 99 | |
|
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
100 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: |
| 0 | 101 |
| 102 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.* | |
| 103 | |
| 104 | |
| 105 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example: | |
| 106 | |
| 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* | |
| 108 | |
| 109 | |
| 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: | |
| 111 | |
| 112 - Hom/Het case = "hom" | |
| 113 | |
|
2
bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents:
1
diff
changeset
|
114 - Hom/Het control = "any" |
| 0 | 115 |
| 116 - Case / Control column designation = ""++++------" | |
| 117 | |
| 118 | |
| 119 @EXTERNAL_DOCUMENTATION@ | |
| 120 http://snpeff.sourceforge.net/SnpSift.html#casecontrol | |
| 121 | |
|
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
0
diff
changeset
|
122 ]]> |
|
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
0
diff
changeset
|
123 </help> |
|
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents:
0
diff
changeset
|
124 <expand macro="citations" /> |
| 0 | 125 </tool> |