diff tools/rgenetics/rgTDT.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/rgTDT.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,108 @@
+<tool id="rgTDT1" name="Transmission Distortion:">
+    <description>for family data</description>
+
+    <command interpreter="python">
+        rgTDT.py -i '$i.extra_files_path/$i.metadata.base_name' -o '$title'
+        -r '$out_file1' -l '$logf'  -g '$gffout'
+    </command>
+
+    <inputs>
+       <param name="i"  type="data" label="Genotypes for analysis from your current history datasets"
+          size="132" format="pbed" />
+       <param name='title' type='text' value='rgTDT'  label="Title for the output to remind you what you did" size="80"/>
+   </inputs>
+
+   <outputs>
+       <data format="tabular" name="out_file1" label="${title}_rgTDT.xls"/>
+       <data format="gff" name="gffout" label="${title}_rgTDT.gff"/>
+       <data format="txt" name="logf" label="${title}_rgTDTlog.txt"/>
+   </outputs>
+
+<tests>
+ <test>
+ <param name='i' value='tinywga' ftype='pbed' >
+   <metadata name='base_name' value='tinywga' />
+   <composite_data value='tinywga.bim' />
+   <composite_data value='tinywga.bed' />
+   <composite_data value='tinywga.fam' />
+   <edit_attributes type='name' value='tinywga' /> 
+ </param>
+ <param name='title' value='rgTDTtest1' />
+ <output name='out_file1' file='rgTDTtest1_TDT.xls' ftype='tabular' compare="diff"/>
+ <output name='gffout' file='rgTDTtest1_TDT_topTable.gff' ftype='gff' compare="diff" />
+ <output name='logf' file='rgTDTtest1_TDT_log.txt' ftype='txt' lines_diff='79'/>
+ </test>
+</tests>
+
+
+<help>
+
+.. class:: infomark
+
+**Attribution**
+
+This tool relies on the work of many people. It uses Plink http://pngu.mgh.harvard.edu/~purcell/plink/ for
+analysis, and the R http://cran.r-project.org/ for graphics respectively.
+
+This implementation is a Galaxy tool wrapper around these third party applications.
+It was originally designed and written for family based data from the CAMP Illumina run of 2007 by
+ross lazarus ([e-mail]) and incorporated into the rgenetics toolkit.
+
+Rgenetics merely exposes them, wrapping Plink so you can use it in Galaxy.
+
+-----
+
+.. class:: infomark
+
+**Syntax**
+
+- **Genotype file** is the input family data chosen from available library compressed files
+- **Format** determines how your data will be returned to your Galaxy workspace - the gg format is strongly recommended
+
+-----
+
+.. class:: infomark
+
+**Summary**
+
+This tool will perform the standard transmission distortion analyses suitable for
+nuclear families and a simple binary "affected" phenotype
+
+If you don't see the genotype data set you want here, it can be imported using one of the methods available from
+the Galaxy Get Data tool page.
+
+Outputs will include a GFF toptable with a link to view at UCSC if you want to see your
+results as a fully fledged UCSC track.
+
+Finally, if you can't live without
+spreadsheet data, choose the .xls tab delimited format. It's not a stupid binary excel file. Just a plain old tab delimited
+one with a header. Fortunately excel is dumb enough to open these without much protest.
+
+
+----
+
+.. class:: infomark
+
+**Attribution**
+
+This Galaxy tool relies on Plink (see Plinksrc_) to test TDT models. 
+
+So, we rely on the author (Shaun Purcell) for the documentation you need specific to those settings - they are very nicely documented - see
+DOC_
+
+Tool and Galaxy datatypes originally designed and written for the Rgenetics
+series of whole genome scale statistical genetics tools by ross lazarus ([e-mail])
+
+Copyright Ross Lazarus March 2007
+This Galaxy wrapper is released licensed under the LGPL_ but is about as useful as a chocolate teapot without Plink which is GPL.
+
+I'm no lawyer, but it looks like you got GPL if you use this software. Good luck.
+
+.. _Plinksrc: http://pngu.mgh.harvard.edu/~purcell/plink/ 
+
+.. _LGPL: http://www.gnu.org/copyleft/lesser.html
+
+.. _DOC: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#tdt
+
+</help>
+</tool>