diff dpmix.xml @ 31:a631c2f6d913

Update to Miller Lab devshed revision 3c4110ffacc3

--- a/dpmix.xml	Fri Jul 26 12:51:13 2013 -0400
+++ b/dpmix.xml	Fri Sep 20 13:25:27 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="gd_dpmix" name="Admixture" version="1.1.0">
+<tool id="gd_dpmix" name="Admixture" version="1.2.0">
   <description>: Map genomic intervals resembling specified source populations</description>
 
   <command interpreter="python">
@@ -31,7 +31,13 @@
     #else if $user_het.choice == '2'
       #set $het_arg = 'use_none'
     #end if
-    '$switch_penalty' '$ap1_input' '$ap1_input.name' '$ap2_input' '$ap2_input.name' '$ap3_arg' '$ap3_name_arg' '$p_input' '$output' '$output2' '$output2.files_path' '$input.dataset.metadata.dbkey' '$input.dataset.metadata.ref' '$GALAXY_DATA_INDEX_DIR' 'gd.heterochromatic.loc' '$ind_arg' '$het_arg' '1'
+    '$switch_penalty'
+    #if $use_reference.choice == '0'
+      '$ap1_input' '$ap1_input.name'
+    #else if $use_reference.choice == '1'
+      '/dev/null' 'reference'
+    #end if
+    '$ap2_input' '$ap2_input.name' '$ap3_arg' '$ap3_name_arg' '$p_input' '$output' '$output2' '$output2.files_path' '$input.dataset.metadata.dbkey' '$input.dataset.metadata.ref' '$GALAXY_DATA_INDEX_DIR' 'gd.heterochromatic.loc' '$ind_arg' '$het_arg' '$add_logs'
   </command>
 
   <inputs>
@@ -57,7 +63,17 @@
       </when>
     </conditional>
 
-    <param name="ap1_input" type="data" format="gd_indivs" label="Source population 1 individuals" />
+    <conditional name="use_reference">
+      <param name="choice" type="select" format="integer" label="History item or Reference sequence">
+        <option value="0" selected="true">History item</option>
+        <option value="1">Reference sequence</option>
+      </param>
+      <when value="0">
+        <param name="ap1_input" type="data" format="gd_indivs" label="Source population 1 individuals" />
+      </when>
+      <when value="1" />
+    </conditional>
+
     <param name="ap2_input" type="data" format="gd_indivs" label="Source population 2 individuals" />
 
     <conditional name="third_pop">
@@ -87,12 +103,10 @@
       </when>
     </conditional>
 
-    <!--
     <param name="add_logs" type="select" format="integer" label="Probabilities">
       <option value="1" selected="true">add logs of probabilities</option>
       <option value="0">add probabilities</option>
     </param>
-    -->
 
   </inputs>
 
@@ -101,6 +115,11 @@
     <data name="output2" format="html" />
   </outputs>
 
+  <requirements>
+    <requirement type="package" version="0.1">gd_c_tools</requirement>
+    <requirement type="package" version="1.2.1">matplotlib</requirement>
+  </requirements>
+
   <tests>
     <test>
       <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" />