--- a/dpmix.xml	Wed May 22 15:58:18 2013 -0400
+++ b/dpmix.xml	Tue May 28 16:24:19 2013 -0400
@@ -1,8 +1,14 @@
-<tool id="gd_dpmix" name="Admixture" version="1.0.0">
+<tool id="gd_dpmix" name="Admixture" version="1.1.0">
   <description>: Map genomic intervals resembling specified ancestral populations</description>
 
   <command interpreter="python">
-    dpmix.py "$input" "$data_source" "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc"
+    dpmix.py "$input"
+    #if $input_type.choice == '0'
+      "gd_snp" "$input_type.data_source"
+    #else if $input_type.choice == '1'
+      "gd_genotype" "1"
+    #end if
+    "$switch_penalty" "$ap1_input" "$ap2_input" "$p_input" "$output" "$output2" "$output2.files_path" "$input.dataset.metadata.dbkey" "$input.dataset.metadata.ref" "$GALAXY_DATA_INDEX_DIR" "gd.heterochromatic.loc"
     #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
       #set $arg = '%s:%s' % ($individual_col, $individual)
       "$arg"
@@ -10,18 +16,32 @@
   </command>
 
   <inputs>
-    <param name="input" type="data" format="gd_snp" label="SNP dataset">
-      <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
-    </param>
+    <conditional name="input_type">
+      <param name="choice" type="select" format="integer" label="Input format">
+        <option value="0" selected="true">gd_snp</option>
+        <option value="1">gd_genotype</option>
+      </param>
+      <when value="0">
+        <param name="input" type="data" format="gd_snp" label="SNP dataset">
+          <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
+        </param>
+
+        <param name="data_source" type="select" format="integer" label="Similarity metric">
+          <option value="0">sequence coverage</option>
+          <option value="1" selected="true">estimated genotype</option>
+        </param>
+      </when>
+      <when value="1">
+        <param name="input" type="data" format="gd_genotype" label="Genotype dataset">
+          <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" />
+        </param>
+      </when>
+    </conditional>
+
     <param name="ap1_input" type="data" format="gd_indivs" label="Ancestral population 1 individuals" />
     <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="data_source" type="select" format="integer" label="Similarity metric">
-      <option value="0" selected="true">sequence coverage</option>
-      <option value="1">estimated genotype</option>
-    </param>
-
     <param name="switch_penalty" type="integer" min="0" value="10" label="Genotype switch penalty" help="Note: typically between 10 and 100."/>
   </inputs>
 
@@ -52,13 +72,14 @@
 
 **Dataset formats**
 
-The input datasets are in gd_snp_ and gd_indivs_ formats.  It is important for
+The input datasets are in gd_snp_, gd_genotype_, and gd_indivs_ formats.  It is important for
 the Individuals datasets to have unique names and for there to be no overlap
 between the two populations.  Rename these datasets if
 needed to make them unique.  
 There are two output datasets, one tabular_ and one composite. (`Dataset missing?`_)
 
 .. _gd_snp: ./static/formatHelp.html#gd_snp
+.. _gd_genotype: ./static/formatHelp.html#gd_genotype
 .. _gd_indivs: ./static/formatHelp.html#gd_indivs
 .. _tabular: ./static/formatHelp.html#tab
 .. _Dataset missing?: ./static/formatHelp.html