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/tools/rgenetics/rgTDT.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool id="rgTDT1" name="Transmission Distortion:">
  2    <description>for family data</description>
  3
  4    <command interpreter="python">
  5        rgTDT.py -i '$i.extra_files_path/$i.metadata.base_name' -o '$title'
  6        -r '$out_file1' -l '$logf'  -g '$gffout'
  7    </command>
  8
  9    <inputs>
 10       <param name="i"  type="data" label="Genotypes for analysis from your current history datasets"
 11          size="132" format="pbed" />
 12       <param name='title' type='text' value='rgTDT'  label="Title for the output to remind you what you did" size="80"/>
 13   </inputs>
 14
 15   <outputs>
 16       <data format="tabular" name="out_file1" label="${title}_rgTDT.xls"/>
 17       <data format="gff" name="gffout" label="${title}_rgTDT.gff"/>
 18       <data format="txt" name="logf" label="${title}_rgTDTlog.txt"/>
 19   </outputs>
 20
 21<tests>
 22 <test>
 23 <param name='i' value='tinywga' ftype='pbed' >
 24   <metadata name='base_name' value='tinywga' />
 25   <composite_data value='tinywga.bim' />
 26   <composite_data value='tinywga.bed' />
 27   <composite_data value='tinywga.fam' />
 28   <edit_attributes type='name' value='tinywga' /> 
 29 </param>
 30 <param name='title' value='rgTDTtest1' />
 31 <output name='out_file1' file='rgTDTtest1_TDT.xls' ftype='tabular' compare="diff"/>
 32 <output name='gffout' file='rgTDTtest1_TDT_topTable.gff' ftype='gff' compare="diff" />
 33 <output name='logf' file='rgTDTtest1_TDT_log.txt' ftype='txt' lines_diff='79'/>
 34 </test>
 35</tests>
 36
 37
 38<help>
 39
 40.. class:: infomark
 41
 42**Attribution**
 43
 44This tool relies on the work of many people. It uses Plink http://pngu.mgh.harvard.edu/~purcell/plink/ for
 45analysis, and the R http://cran.r-project.org/ for graphics respectively.
 46
 47This implementation is a Galaxy tool wrapper around these third party applications.
 48It was originally designed and written for family based data from the CAMP Illumina run of 2007 by
 49ross lazarus (ross.lazarus@gmail.com) and incorporated into the rgenetics toolkit.
 50
 51Rgenetics merely exposes them, wrapping Plink so you can use it in Galaxy.
 52
 53-----
 54
 55.. class:: infomark
 56
 57**Syntax**
 58
 59- **Genotype file** is the input family data chosen from available library compressed files
 60- **Format** determines how your data will be returned to your Galaxy workspace - the gg format is strongly recommended
 61
 62-----
 63
 64.. class:: infomark
 65
 66**Summary**
 67
 68This tool will perform the standard transmission distortion analyses suitable for
 69nuclear families and a simple binary "affected" phenotype
 70
 71If you don't see the genotype data set you want here, it can be imported using one of the methods available from
 72the Galaxy Get Data tool page.
 73
 74Outputs will include a GFF toptable with a link to view at UCSC if you want to see your
 75results as a fully fledged UCSC track.
 76
 77Finally, if you can't live without
 78spreadsheet data, choose the .xls tab delimited format. It's not a stupid binary excel file. Just a plain old tab delimited
 79one with a header. Fortunately excel is dumb enough to open these without much protest.
 80
 81
 82----
 83
 84.. class:: infomark
 85
 86**Attribution**
 87
 88This Galaxy tool relies on Plink (see Plinksrc_) to test TDT models. 
 89
 90So, we rely on the author (Shaun Purcell) for the documentation you need specific to those settings - they are very nicely documented - see
 91DOC_
 92
 93Tool and Galaxy datatypes originally designed and written for the Rgenetics
 94series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus@gmail.com)
 95
 96Copyright Ross Lazarus March 2007
 97This Galaxy wrapper is released licensed under the LGPL_ but is about as useful as a chocolate teapot without Plink which is GPL.
 98
 99I'm no lawyer, but it looks like you got GPL if you use this software. Good luck.
100
101.. _Plinksrc: http://pngu.mgh.harvard.edu/~purcell/plink/ 
102
103.. _LGPL: http://www.gnu.org/copyleft/lesser.html
104
105.. _DOC: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#tdt
106
107</help>
108</tool>