# HG changeset patch
# User wolma
# Date 1421422928 18000
# Node ID e81a2448d1fbb59ac796fd8b6214280b587a920e
# Parent  17ea8fd2ca18629a0dddc689f0211e53e0b9c5c2
upgrade to v0.1.5.1

diff -r 17ea8fd2ca18 -r e81a2448d1fb cloudmap.xml
--- a/cloudmap.xml	Sat Dec 13 17:20:01 2014 -0500
+++ b/cloudmap.xml	Fri Jan 16 10:42:08 2015 -0500
@@ -1,13 +1,10 @@
 <tool id="cloudmap_prepare" name="Prepare variant data for mapping">
   <description>with the CloudMap series of tools.</description>
-  <requirements>
-    <requirement type="package" version="0.1.5">mimodd</requirement>
-  </requirements>
   <version_command>mimodd version -q</version_command>
   <command>
     mimodd cloudmap "$ifile" ${run.mode} 
     
-    #if $str($run.mode) != "EMS":
+    #if $str($run.mode) != "SVD":
         "${run.refsample}"
     #end if
     
@@ -22,18 +19,14 @@
     <param name="ifile" type="data" format="vcf" label="vcf input file" />
     <conditional name="run">
       <param name="mode" type="select" label="CloudMap analysis to prepare data for">
-        <option value="EMS">EMS Variant Density Mapping</option>
-        <option value="VARIANT">Variant Discovery Mapping</option>
-        <option value="HAWAIIAN">Hawaiian Variant Mapping</option>
+        <option value="SVD">EMS Variant Density Mapping</option>
+        <option value="VAF">Variant Discovery / Hawaiian Variant Mapping</option>
       </param>
-      <when value="EMS">
+      <when value="SVD">
         <param name="refsample" type="hidden" value="None" />
       </when>
-      <when value="VARIANT">
-        <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be EXCLUDED from the analysis" />
-      </when>
-      <when value="HAWAIIAN">
-        <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides crossing strain variants to be INCLUDED in the analysis" />
+      <when value="VAF">
+        <param name="refsample" type="text" label="name of the reference sample" help="the sample that provides mapping strain variants" />
       </when>
     </conditional>
     <param name="sample" type="text" label="subject sample name" help="the sample to perform CloudMap mapping for" />
@@ -42,7 +35,7 @@
   </inputs>
 
   <outputs>
-    <data name="ofile" format="vcf" label="CloudMap ${run.mode} Mapping-ready VCF File from ${on_string}" />
+    <data name="ofile" format="vcf" label="CloudMap-ready ${run.mode} File from ${on_string}" />
     <data name="dictfile" format="tabular" label="Species Configuration File for CloudMap from ${on_string}">
       <filter>seqdict</filter>
     </data>
diff -r 17ea8fd2ca18 -r e81a2448d1fb tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Dec 13 17:20:01 2014 -0500
+++ b/tool_dependencies.xml	Fri Jan 16 10:42:08 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="mimodd" version="0.1.5">
-      <repository changeset_revision="fbac402764d6" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="mimodd" version="0.1.5">
+        <repository changeset_revision="a1ed24182b03" name="package_mimodd_0_1_5" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>