--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/rgCaCo.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,103 @@
+<tool id="rgCaCo1" name="Case Control:">
+    <description>for unrelated subjects</description>
+    <command interpreter="python">
+        rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title"  '$out_file1' '$logf' '$logf.files_path' '$gffout'
+    </command>
+    <inputs>
+      <param name="i"  type="data" label="RGenetics genotype data from your current history"
+      format="pbed" />
+       <param name='title' type='text' size="132" value='CaseControl' label="Title for this job"/>
+
+    </inputs>
+
+   <outputs>
+       <data format="tabular" name="out_file1" label="${title}_rgCaCo.xls" />
+       <data format="txt" name="logf" label="${title}_rgCaCo.log"/>
+       <data format="gff" name="gffout" label="${title}_rgCaCoTop.gff" />
+   </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='rgCaCotest1' />
+ <output name='out_file1' file='rgCaCotest1_CaCo.xls' ftype='tabular' compare='diff' />
+ <output name='logf' file='rgCaCotest1_CaCo_log.txt' ftype='txt' compare='diff' lines_diff='20' />
+ <output name='gffout' file='rgCaCotest1_CaCo_topTable.gff' ftype='gff' compare='diff' />
+ </test>
+</tests>
+<help>
+
+.. class:: infomark
+
+**Syntax**
+
+- **Genotype file** is the input case control data chosen from available library Plink binary files
+- **Map file** is the linkage format .map file corresponding to the genotypes in the Genotype file
+- **Type of test** is the kind of test statistic to report such as Armitage trend test or genotype test
+- **Format** determines how your data will be returned to your Galaxy workspace
+
+-----
+
+**Summary**
+
+This tool will perform some standard statistical tests comparing subjects designated as
+affected (cases) and unaffected subjects (controls). To avoid bias, it is important that
+controls who had been affected would have been eligible for sampling as cases. This may seem
+odd, but it requires that the cases and controls are drawn from the same sampling frame.
+
+The armitage trend test is robust to departure from HWE and so very attractive - after all, a real disease
+mutation may well result in distorted HWE at least in cases. All the others are susceptible to
+bias in the presence of HWE departures.
+
+All of these tests are exquisitely sensitive to non-differential population stratification in cases
+compared to controls and this must be tested before believing any results here. Use the PCA method for
+100k markers or more.
+
+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.
+
+Output format can be UCSC .bed if you want to see your
+results as a fully fledged UCSC track. A map file containing the chromosome and offset for each marker is required for
+writing this kind of output.
+Alternatively you can use .gg for the UCSC Genome Graphs tool which has all of the advantages
+of the the .bed track, plus a neat, visual front end that displays a lot of useful clues.
+Either of these are a very useful way of quickly getting a look
+at your data in full genomic context.
+
+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 Casae Control association 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 (ross.lazarus@gmail.com)
+
+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#cc
+
+</help>
+</tool>