[2] | 1 | <tool id="rgTDT1" name="Transmission Distortion:"> |
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| 2 | <code file="rgTDT_code.py"/> |
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| 3 | |
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| 4 | <description>for family data</description> |
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| 5 | |
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| 6 | <command interpreter="python"> |
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| 7 | rgTDT.py -i '$i.extra_files_path/$i.metadata.base_name' -o '$title1' |
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| 8 | -r '$out_file1' -l '$logf' -g '$gffout' |
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| 9 | </command> |
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| 10 | |
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| 11 | <inputs> |
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| 12 | <param name="i" type="data" label="Genotypes for analysis from your current history datasets" |
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| 13 | size="132" format="pbed" /> |
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| 14 | <param name='title1' type='text' value='rgTDT' size="80"/> |
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| 15 | </inputs> |
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| 16 | |
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| 17 | <outputs> |
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| 18 | <data format="tabular" name="out_file1" /> |
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| 19 | <data format="gff" name="gffout" /> |
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| 20 | <data format="txt" name="logf" /> |
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| 21 | </outputs> |
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| 22 | |
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| 23 | <tests> |
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| 24 | <test> |
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| 25 | <param name='i' value='tinywga' ftype='pbed' > |
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| 26 | <metadata name='base_name' value='tinywga' /> |
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| 27 | <composite_data value='tinywga.bim' /> |
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| 28 | <composite_data value='tinywga.bed' /> |
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| 29 | <composite_data value='tinywga.fam' /> |
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| 30 | <edit_attributes type='name' value='tinywga' /> |
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| 31 | </param> |
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| 32 | <param name='title1' value='rgTDTtest1' /> |
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| 33 | <output name='out_file1' file='rgTDTtest1_TDT.xls' ftype='tabular' compare="diff"/> |
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| 34 | <output name='gffout' file='rgTDTtest1_TDT_topTable.gff' ftype='gff' compare="diff" /> |
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| 35 | <output name='logf' file='rgTDTtest1_TDT_log.txt' ftype='txt' lines_diff='79'/> |
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| 36 | </test> |
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| 37 | </tests> |
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| 38 | |
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| 39 | |
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| 40 | <help> |
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| 41 | |
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| 42 | .. class:: infomark |
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| 43 | |
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| 44 | **Attribution** |
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| 45 | |
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| 46 | This tool relies on the work of many people. It uses Plink http://pngu.mgh.harvard.edu/~purcell/plink/ for |
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| 47 | analysis, and the R http://cran.r-project.org/ for graphics respectively. |
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| 48 | |
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| 49 | This implementation is a Galaxy tool wrapper around these third party applications. |
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| 50 | It was originally designed and written for family based data from the CAMP Illumina run of 2007 by |
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| 51 | ross lazarus (ross.lazarus@gmail.com) and incorporated into the rgenetics toolkit. |
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| 52 | |
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| 53 | Rgenetics merely exposes them, wrapping Plink so you can use it in Galaxy. |
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| 54 | |
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| 55 | ----- |
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| 56 | |
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| 57 | .. class:: infomark |
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| 58 | |
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| 59 | **Syntax** |
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| 60 | |
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| 61 | - **Genotype file** is the input family data chosen from available library compressed files |
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| 62 | - **Format** determines how your data will be returned to your Galaxy workspace - the gg format is strongly recommended |
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| 63 | |
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| 64 | ----- |
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| 65 | |
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| 66 | .. class:: infomark |
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| 67 | |
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| 68 | **Summary** |
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| 69 | |
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| 70 | This tool will perform the standard transmission distortion analyses suitable for |
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| 71 | nuclear families and a simple binary "affected" phenotype |
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| 72 | |
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| 73 | 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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| 74 | the Galaxy Get Data tool page. |
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| 75 | |
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| 76 | Outputs will include a GFF toptable with a link to view at UCSC if you want to see your |
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| 77 | results as a fully fledged UCSC track. |
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| 78 | |
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| 79 | Finally, if you can't live without |
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| 80 | 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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| 81 | one with a header. Fortunately excel is dumb enough to open these without much protest. |
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| 82 | |
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| 83 | |
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| 84 | </help> |
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| 85 | </tool> |
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