root/galaxy-central/tools/rgenetics/rgGTOOL.xml

<tool id="rgGTOOL1" name="Converter">
    <code file="listFiles.py"/> 
    <code file="rgGTOOL_code.py"/> 
  
    <description>from linkage format to SNPTEST Marchini files</description>
  
    <command interpreter="python">
        rgGTOOL.py $i $o $discrete $logf $outdir
    </command>
    
    <inputs>    
       <param name="i"  type="select" label="Genotype file" dynamic_options="get_lib_pedfiles()" /> 
       <param name="discrete" type="select" label="Make Case/Control based on affection 2/1">
                        <option selected="yes" value="1">Discrete</option>
                        <option value="0">Continuous</option>
       </param>
       <param name="o" type="text" label="Output Marchini format name" value="Marchini"/>
       <param name="outdir" type="hidden" value="/usr/local/galaxy/data/rg/snptest" />
   </inputs>

   <outputs>  
       <data format="txt" name="logf"  />
   </outputs>
<help>


**Syntax**

- **Genotype file** is the input linkage format pedigree and corresponding map file
- **Discrete** is the type of phenotype in the affection column 
- **Output name** is the file name (.gen and .sample will be added) for the new SNPTEST compatible file

**Note on Discrete**
See GTOOL_ documentation link below for more details. Briefly, if
your linkage format pedigree file has 1/2 in column 6 for control/case respectively, setting this to Yes will create two 
complete sets of output files distinguished by 1 and 2 respectively. otherwise, affection status is assumed to contain a 
continuous phenotype and a single output set is produced


**Summary**

Code used here from Jonathon Marchini's group - see documentation at GTOOL_.

.. _GTOOL: http://www.stats.ox.ac.uk/~marchini/software/gwas/gtool.html

-----

**Attribution**
Originally designed and written for the Rgenetics
series of Galaxy tools by ross lazarus (ross.lazarus@gmail.com), who didn't write GTOOL_
but wishes he had.

</help>
</tool>