<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>