view tools/rgenetics/rgGTOOL.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<tool id="rgGTOOL1" name="Converter">

    <description>from linkage format to SNPTEST Marchini files</description>
    <command interpreter="python"> $i $o $discrete $logf $outdir
       <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 name="o" type="text" label="Output Marchini format name" value="Marchini"/>
       <param name="outdir" type="hidden" value="/usr/local/galaxy/data/rg/snptest" />

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


- **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


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

.. _GTOOL:


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