# HG changeset patch
# User Richard Burhans <burhans@bx.psu.edu>
# Date 1369849759 14400
# Node ID cba0d7a63b82616d7e7639f69dc9c04b86c46d15
# Parent  248b06e86022708978f7dab5c3f4502052e4904d
workaround for gd_genotype datatype
admix shift int -> float

diff -r 248b06e86022 -r cba0d7a63b82 datatypes_conf.xml
--- a/datatypes_conf.xml	Tue May 28 16:24:19 2013 -0400
+++ b/datatypes_conf.xml	Wed May 29 13:49:19 2013 -0400
@@ -7,7 +7,7 @@
     <datatype extension="gd_indivs" type="galaxy.datatypes.wsf:Individuals" display_in_upload="true"/>
     <datatype extension="gd_ped" type="galaxy.datatypes.wsf:Wped" display_in_upload="true"/>
     <datatype extension="gd_snp" type="galaxy.datatypes.wsf:GDSnp" display_in_upload="true"/>
-    <datatype extension="gd_genotype" type="galaxy.datatypes.wsf:GDSnp" subclass="true" display_in_upload="true"/>
+    <datatype extension="gd_genotype" type="galaxy.datatypes.wsf:GDGenotype" display_in_upload="true"/>
     <datatype extension="gd_sap" type="galaxy.datatypes.wsf:GDSap" display_in_upload="true"/>
     <datatype extension="gd_covered_cds" type="galaxy.datatypes.interval:Interval" subclass="true" display_in_upload="true"/>
   </registration>
diff -r 248b06e86022 -r cba0d7a63b82 dpmix.xml
--- a/dpmix.xml	Tue May 28 16:24:19 2013 -0400
+++ b/dpmix.xml	Wed May 29 13:49:19 2013 -0400
@@ -42,7 +42,7 @@
     <param name="ap2_input" type="data" format="gd_indivs" label="Ancestral population 2 individuals" />
     <param name="p_input" type="data" format="gd_indivs" label="Potentially admixed individuals" />
 
-    <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/>
+    <param name="switch_penalty" type="float" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/>
   </inputs>
 
   <outputs>
diff -r 248b06e86022 -r cba0d7a63b82 lib/galaxy/datatypes/wsf.py
--- a/lib/galaxy/datatypes/wsf.py	Tue May 28 16:24:19 2013 -0400
+++ b/lib/galaxy/datatypes/wsf.py	Wed May 29 13:49:19 2013 -0400
@@ -176,6 +176,10 @@
             dataset.metadata.individual_names = individual_names[:]
             dataset.metadata.individual_columns = individual_columns[:]
 
+class GDGenotype( GDSnp ):
+    """ Webb's genotype file format """
+    file_ext = 'gd_genotype'
+
 class GDSap( Fake ):
     """ Webb's SAP file format """
     file_ext = 'gd_sap'