From c8a71a49f865f2141eaf8be341f42e5ba14f445d Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Mon, 1 Dec 2008 13:24:01 -0500
Subject: [PATCH] Add RGenetic datatypes to datatypes.conf.sample and remove
 the always true sniff method of SNPMatrix

---
 datatypes_conf.xml.sample        | 24 ++++++++++++++++++++++++
 lib/galaxy/datatypes/genetics.py |  8 ++++----
 2 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/datatypes_conf.xml.sample b/datatypes_conf.xml.sample
index 7db33f2e7d7..23974aab8b6 100644
--- a/datatypes_conf.xml.sample
+++ b/datatypes_conf.xml.sample
@@ -140,6 +140,30 @@
     <datatype extension="wobble" type="galaxy.datatypes.data:Text"/>
     <datatype extension="wordcount" type="galaxy.datatypes.data:Text"/>
     <datatype extension="tagseq" type="galaxy.datatypes.data:Text"/>
+  <!-- Start RGenetics Datatypes -->
+    <!-- genome graphs ucsc file - first col is always marker then numeric values to plot -->
+    <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>
+    <datatype extension="rgenetics" type="galaxy.datatypes.genetics:Rgenetics"/>
+    <!-- linkage format pedigree (separate .map file) -->
+    <datatype extension="lped" type="galaxy.datatypes.genetics:Lped"/>
+    <!-- plink compressed file - has bed extension unfortunately -->
+    <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed"/>
+    <!-- eigenstrat pedigree input file -->
+    <datatype extension="eigenstratgeno" type="galaxy.datatypes.genetics:Eigenstratgeno"/>
+    <!-- eigenstrat pca output file for adjusted eigenQTL eg -->
+    <datatype extension="eigenstratpca" type="galaxy.datatypes.genetics:Eigenstratpca"/>
+    <!-- fbat/pbat format pedigree (header row of marker names) -->
+    <datatype extension="fped" type="galaxy.datatypes.genetics:Fped"/>
+    <!-- part of linkage format pedigree -->
+    <datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap"/>
+    <!-- phenotype file - fbat format -->
+    <datatype extension="fphe" type="galaxy.datatypes.genetics:Fphe"/>
+    <!-- phenotype file - plink format -->
+    <datatype extension="pphe" type="galaxy.datatypes.genetics:Pphe"/>
+    <datatype extension="snptest" type="galaxy.datatypes.genetics:Snptest"/>
+    <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix"/>
+    <datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/>
+  <!-- End RGenetics Datatypes -->
   </registration>
   <sniffers>
     <!--
diff --git a/lib/galaxy/datatypes/genetics.py b/lib/galaxy/datatypes/genetics.py
index 9857eb7d36d..27032ecc2b2 100644
--- a/lib/galaxy/datatypes/genetics.py
+++ b/lib/galaxy/datatypes/genetics.py
@@ -132,10 +132,10 @@ class SNPMatrix(Rgenetics):
     def set_peek( self, dataset ):
         dataset.peek  = "Binary RGenetics file"
         dataset.blurb = data.nice_size( dataset.get_size() )
-    def sniff( self, filename ):
-        """
-        """
-        return True
+    #def sniff( self, filename ):
+    #    """
+    #    """
+    #    return True
 
 class Lped(Rgenetics):
     """fake class to distinguish different species of Rgenetics data collections