[2] | 1 | <tool id="rgCaCo1" name="Case Control:"> |
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| 2 | <code file="listFiles.py"/> |
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| 3 | <code file="rgCaCo_code.py"/> |
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| 4 | |
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| 5 | <description>for unrelated subjects</description> |
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| 6 | |
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| 7 | <command interpreter="python"> |
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| 8 | rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name" |
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| 9 | '$out_file1' '$logf' '$logf.files_path' '$gffout' |
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| 10 | </command> |
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| 11 | |
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| 12 | <inputs> |
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| 13 | <param name="i" type="data" label="RGenetics genotype data from your current history" |
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| 14 | format="pbed" /> |
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| 15 | <param name='name' type='text' size="132" value='CaseControl' label="Title for this job"/> |
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| 16 | |
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| 17 | </inputs> |
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| 18 | |
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| 19 | <outputs> |
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| 20 | <data format="tabular" name="out_file1" /> |
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| 21 | <data format="txt" name="logf" /> |
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| 22 | <data format="gff" name="gffout" /> |
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| 23 | </outputs> |
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| 24 | <tests> |
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| 25 | <test> |
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| 26 | <param name='i' value='tinywga' ftype='pbed' > |
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| 27 | <metadata name='base_name' value='tinywga' /> |
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| 28 | <composite_data value='tinywga.bim' /> |
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| 29 | <composite_data value='tinywga.bed' /> |
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| 30 | <composite_data value='tinywga.fam' /> |
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| 31 | <edit_attributes type='name' value='tinywga' /> |
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| 32 | </param> |
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| 33 | <param name='name' value='rgCaCotest1' /> |
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| 34 | <output name='out_file1' file='rgCaCotest1_CaCo.xls' ftype='tabular' compare='diff' /> |
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| 35 | <output name='logf' file='rgCaCotest1_CaCo_log.txt' ftype='txt' compare='diff' lines_diff='20' /> |
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| 36 | <output name='gffout' file='rgCaCotest1_CaCo_topTable.gff' ftype='gff' compare='diff' /> |
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| 37 | </test> |
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| 38 | </tests> |
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| 39 | <help> |
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| 40 | |
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| 41 | .. class:: infomark |
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| 42 | |
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| 43 | **Syntax** |
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| 44 | |
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| 45 | - **Genotype file** is the input case control data chosen from available library Plink binary files |
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| 46 | - **Map file** is the linkage format .map file corresponding to the genotypes in the Genotype file |
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| 47 | - **Type of test** is the kind of test statistic to report such as Armitage trend test or genotype test |
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| 48 | - **Format** determines how your data will be returned to your Galaxy workspace |
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| 49 | |
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| 50 | ----- |
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| 51 | |
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| 52 | **Summary** |
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| 53 | |
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| 54 | This tool will perform some standard statistical tests comparing subjects designated as |
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| 55 | affected (cases) and unaffected subjects (controls). To avoid bias, it is important that |
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| 56 | controls who had been affected would have been eligible for sampling as cases. This may seem |
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| 57 | odd, but it requires that the cases and controls are drawn from the same sampling frame. |
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| 58 | |
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| 59 | The armitage trend test is robust to departure from HWE and so very attractive - after all, a real disease |
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| 60 | mutation may well result in distorted HWE at least in cases. All the others are susceptible to |
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| 61 | bias in the presence of HWE departures. |
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| 62 | |
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| 63 | All of these tests are exquisitely sensitive to non-differential population stratification in cases |
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| 64 | compared to controls and this must be tested before believing any results here. Use the PCA method for |
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| 65 | 100k markers or more. |
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| 66 | |
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| 67 | If you don't see the genotype data set you want here, it can be imported using one of the methods available from |
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| 68 | the Galaxy Get Data tool page. |
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| 69 | |
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| 70 | Output format can be UCSC .bed if you want to see your |
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| 71 | results as a fully fledged UCSC track. A map file containing the chromosome and offset for each marker is required for |
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| 72 | writing this kind of output. |
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| 73 | Alternatively you can use .gg for the UCSC Genome Graphs tool which has all of the advantages |
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| 74 | of the the .bed track, plus a neat, visual front end that displays a lot of useful clues. |
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| 75 | Either of these are a very useful way of quickly getting a look |
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| 76 | at your data in full genomic context. |
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| 77 | |
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| 78 | Finally, if you can't live without |
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| 79 | spreadsheet data, choose the .xls tab delimited format. It's not a stupid binary excel file. Just a plain old tab delimited |
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| 80 | one with a header. Fortunately excel is dumb enough to open these without much protest. |
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| 81 | |
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| 82 | ----- |
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| 83 | |
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| 84 | **Attribution** |
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| 85 | |
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| 86 | When you click 'execute', this Galaxy tool will run Plink (from Shaun Purcell) for you (which is GPL, so this must be too I guess) for calculations. For full Plink |
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| 87 | attribution, source code and documentation, please see http://pngu.mgh.harvard.edu/~purcell/plink/ |
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| 88 | |
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| 89 | The Plink output files will be adjusted into UCSC compatible tracks - gg or wig, or else as tab delimited |
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| 90 | for you spreadsheet junkies out there. Python is used for all glue and data format yoga. |
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| 91 | Originally designed and written for the Rgenetics Galaxy tools by |
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| 92 | ross lazarus (ross spot lazarus ate gmail spot com), who didn't write |
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| 93 | either Galaxy or Plink but wishes he had. |
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| 94 | |
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| 95 | copyright Ross Lazarus 2007 |
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| 96 | Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html |
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| 97 | but is about as useful as a chocolate teapot without Plink which is GPL. |
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| 98 | |
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| 99 | I'm no lawyer, but it looks like you got GPL if you use this software. Good luck. |
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| 100 | |
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| 101 | </help> |
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| 102 | </tool> |
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