--- a/data_manager/add_ctat_resource_lib.xml	Mon Jul 02 18:13:45 2018 -0400
+++ b/data_manager/add_ctat_resource_lib.xml	Mon Jul 02 18:49:11 2018 -0400
@@ -12,18 +12,24 @@
           python $__tool_directory__/add_ctat_resource_lib.py 
             --output_filename="${out_file}" 
             --display_name="${display_name}" 
-            #if str( $genome_resource_library.download ) == "true":
+            #if str( $genome_resource_library.build_type ) == "download_and_build":
                 --download_url="${genome_resource_library.download_url}" 
                 --download_location="${genome_resource_library.download_destination}"
                 #if str( $genome_resource_library.force_new_download ) == "true":
                     --new_archive_download
                 #end if
-            #else
-                #if str( ${genome_resource_library.needs_build} ) == "true":
-                    --source_location="${genome_resource_library.source_location}"
+            #elif str( ${genome_resource_library.build_type} ) == "build_from_source":
+                --source_location "${genome_resource_library.library_status.source_location}"
+                --build_location "${genome_resource_library.built_library_location}" 
+                #if str( $genome_resource_library.library_status.rebuild ) == "true":
+                    --rebuild
                 #end if
+            #elif str( ${genome_resource_library.build_type} ) == "specify_built_location":
+                --build_location "${genome_resource_library.built_library_location}" 
             #end if
-            --build_location "${genome_resource_library.built_library_location}" 
+            #if str( $gmap_build ) == "true":
+                --gmap_build 
+            #end if
         ]]>
     </command>
     <inputs>
@@ -38,9 +44,12 @@
             </when>
         -->
         <conditional name="genome_resource_library">
-            <param name="download" type="boolean" checked="false" label="Download CTAT Genome Resource Library?">
+            <param name="build_type" type="select" label="Download CTAT Genome Resource Library?">
+                <option value="download_and_build" selected="true">Download from CTAT and build if needed</option>
+                <option value="build_from_source">Build library from local source data</option>
+                <option value="specify_built_location">Specify location of built library</option>
             </param>
-            <when value="true">
+            <when value="download_and_build">
                 <!-- The use of a code block to get dynamic options is now deprecated and discouraged.
                      I am still using it here. The only other way I can think of to do this is to
                      create another data_manager that gets the list of files and puts them into a
@@ -79,17 +88,12 @@
                 <param name="download_destination" type="text" label="Download Destination (full path)" />
                 <param name="force_new_download" type="boolean" checked="false" label="Force New Download?" />
             </when>
-            <when value="false">
-                <conditional name="library_status">
-                    <param name="needs_build" type="boolean" checked="false" label="Build Library from source files?">
-                    </param>
-                    <when value="true">
-                        <param name="source_location" type="text" label="Location of Source Files (full path)" />
-                        <param name="rebuild" type="boolean" checked="false" label="Force new build of Library?" />
-                    </when>
-                    <when value="false">
-                    </when>
-                </conditional>
+            <when value="build_from_source">
+                <param name="source_location" type="text" label="Location of Source Files (full path)" />
+                <param name="built_library_location" type="text" label="Location of the Built Library (full path)" />
+                <param name="rebuild" type="boolean" checked="false" label="Force new build of Library?" />
+            </when>
+            <when value="specify_built_location">
                 <param name="built_library_location" type="text" label="Location of the Built Library (full path)" />
             </when>
         </conditional>