/tools/rgenetics/rgTDT.xml

<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 (ross.lazarus@gmail.com) 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 (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#tdt

</help>
</tool>