Mercurial > repos > iuc > snpsift
annotate snpSift_caseControl.xml @ 13:ed810da439cc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
| author | iuc |
|---|---|
| date | Tue, 07 Jun 2016 09:41:13 -0400 |
| parents | 6bf58286d795 |
| children | 80da7fae14b8 |
| rev | line source |
|---|---|
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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changeset
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1 <tool id="snpSift_caseControl" name="SnpSift CaseControl" version="@WRAPPER_VERSION@.0"> |
| 0 | 2 <description>Count samples are in 'case' and 'control' groups.</description> |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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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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b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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9 <expand macro="requirements" /> |
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b884686a80dc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
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10 <expand macro="stdio" /> |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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11 <expand macro="version_command" /> |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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changeset
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12 <command><![CDATA[ |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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13 java -Xmx1G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" caseControl -q |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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changeset
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14 #if str($name).strip() != '': |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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12
diff
changeset
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15 -name "$name" |
| 0 | 16 #end if |
| 17 #if $ctrl.ctrl_src == 'caseString': | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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18 '$ctrl.caseControlStr' |
| 0 | 19 #else |
| 20 -tfam "$ctrl.tfam" | |
| 21 #end if | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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22 "$input" > "$output" |
|
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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23 ]]> |
| 0 | 24 </command> |
| 25 <inputs> | |
| 26 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/> | |
| 27 <conditional name="ctrl"> | |
| 28 <param name="ctrl_src" type="select" label="Case Control defined in"> | |
| 29 <option value="caseString">Case Control String</option> | |
| 30 <option value="tfam">TFAM file</option> | |
| 31 </param> | |
| 32 <when value="caseString"> | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
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diff
changeset
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33 <param name="caseControlStr" type="text" label="Case / Control column designation" size="50"> |
| 0 | 34 <help> |
| 35 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral | |
| 36 </help> | |
| 37 <validator type="regex" message="must be only plus(+), minus(-), or zero(0) characters">[+-0]+</validator> | |
| 38 </param> | |
| 39 </when> | |
| 40 <when value="tfam"> | |
| 41 <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"/> | |
| 42 </when> | |
| 43 </conditional> | |
| 44 <param name="name" type="text" optional="true" label="name" help="name to append to the 'Cases' or 'Controls' tags"> | |
| 45 <validator type="regex" message="Use only valid ID characters">[_a-zA-Z0-9]+</validator> | |
| 46 </param> | |
| 47 </inputs> | |
| 48 <outputs> | |
| 49 <data format="vcf" name="output" /> | |
| 50 </outputs> | |
| 51 <tests> | |
| 52 <test> | |
| 53 <param name="input" ftype="vcf" value="test.private.01.vcf"/> | |
| 54 <param name="ctrl_src" value="caseString"/> | |
| 55 <param name="caseControlStr" value="--"/> | |
| 56 <output name="output"> | |
| 57 <assert_contents> | |
| 58 <has_text text="Cases=0,0,0;" /> | |
| 59 <has_text text="Controls=0,0,0;" /> | |
| 60 </assert_contents> | |
| 61 </output> | |
| 62 </test> | |
| 63 | |
| 64 <test> | |
| 65 <param name="input" ftype="vcf" value="test.private.02.vcf"/> | |
| 66 <param name="ctrl_src" value="caseString"/> | |
| 67 <param name="caseControlStr" value="--"/> | |
| 68 <output name="output"> | |
| 69 <assert_contents> | |
| 70 <has_text text="Cases=0,0,0;" /> | |
| 71 <has_text text="Controls=2,0,4;" /> | |
| 72 </assert_contents> | |
| 73 </output> | |
| 74 </test> | |
| 75 | |
| 76 <test> | |
| 77 <param name="input" ftype="vcf" value="test.private.02.vcf"/> | |
| 78 <param name="name" value=""/> | |
| 79 <param name="ctrl_src" value="caseString"/> | |
| 80 <param name="caseControlStr" value="-+"/> | |
| 81 <output name="output"> | |
| 82 <assert_contents> | |
| 83 <has_text text="Cases=1,0,2;" /> | |
| 84 <has_text text="Controls=1,0,2;" /> | |
| 85 </assert_contents> | |
| 86 </output> | |
| 87 </test> | |
| 88 </tests> | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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89 <help><![CDATA[ |
| 0 | 90 |
| 91 **SnpSift CaseControl** | |
| 92 | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
12
diff
changeset
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93 Allows you to count how many samples are in 'case' group and a 'control' group. You can count 'homozygous', 'heterozygous' or 'any' variants. |
| 0 | 94 |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
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diff
changeset
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95 Case and control are defined by a string containing plus and minus symbols {'+', '-', '0'} where '+' is case, '-' is control and '0' is neutral. |
| 0 | 96 |
| 97 This command adds two annotations to the VCF file: | |
| 98 | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
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diff
changeset
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99 - **CaseControl**: Two comma separated numbers numbers representing the number of samples that have the variant in the case and the control group. Example: |
| 0 | 100 |
| 101 "CaseControl=3,4" *the variant is present in 3 cases and 4 controls.* | |
| 102 | |
| 103 | |
| 104 - **CaseControlP**: A p-value (Fisher exact test) that the number of cases is N or more. Example: | |
| 105 | |
| 106 "CaseControl=4,0;CaseControlP=3.030303e-02" *in this case the pValue of having 4 or more cases and zero controls is 0.03* | |
| 107 | |
| 108 | |
| 109 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: | |
| 110 | |
| 111 - Hom/Het case = "hom" | |
| 112 | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
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113 - Hom/Het control = "any" |
| 0 | 114 |
| 115 - Case / Control column designation = ""++++------" | |
| 116 | |
| 117 | |
| 118 @EXTERNAL_DOCUMENTATION@ | |
| 119 http://snpeff.sourceforge.net/SnpSift.html#casecontrol | |
| 120 | |
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13
ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
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121 ]]> |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
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122 </help> |
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ed810da439cc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
iuc
parents:
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123 <expand macro="citations" /> |
| 0 | 124 </tool> |