# HG changeset patch
# User trinity_ctat
# Date 1540167844 14400
# Node ID 7b8726fb6a36d86a9b20145cb0bc29445d4672c9
# Parent  f403d561cda95995729a112004fa73b0cb39ed95
retry...

diff -r f403d561cda9 -r 7b8726fb6a36 data_manager/add_ctat_resource_lib.xml
--- a/data_manager/add_ctat_resource_lib.xml	Fri Oct 19 18:01:53 2018 -0400
+++ b/data_manager/add_ctat_resource_lib.xml	Sun Oct 21 20:24:04 2018 -0400
@@ -12,32 +12,48 @@
         <![CDATA[
           python $__tool_directory__/add_ctat_resource_lib.py 
             --output_filename="${out_file}" 
-            --display_name="${display_name}" 
-            #if str($genome_resource_library.build_type) == "build_from_source":
-              --source_location "${genome_resource_library.source_location}"
-              #if str($genome_resource_library.rebuild) == "true":
+            --display_name="${display_name}"            
+            #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
+              #if str( $genome_resource_library.keep_archive ) == "true":
+                --keep_archive
+              #end if
+              #if str( $genome_resource_library.rebuild ) == "true":
                 --new_library_build
               #end if
-              if str($genome_resource_library.build_location) == "true":
-                  --build_location="${genome_resource_library.different_build_location}"
+              if str( $genome_resource_library.specify_build_location.build_location ) == "different_location":
+                  --build_location="${genome_resource_library.specify_build_location.different_build_location}"
               #end if
-            #end if
-            #if str($genome_resource_library.build_type) == "specify_built_location":
+            #elif str( $genome_resource_library.build_type ) == "build_from_source":
+              --source_location "${genome_resource_library.source_location}"
+              #if str( $genome_resource_library.rebuild ) == "true":
+                --new_library_build
+              #end if
+              if str( $genome_resource_library.specify_build_location.build_location ) == "true":
+                  --build_location="${genome_resource_library.specify_build_location.different_build_location}"
+              #end if
+            #elif str( $genome_resource_library.build_type ) == "specify_built_location":
               --build_location="${genome_resource_library.built_library_location}"
             #end if
-            #if str($gmap_options.gmap_build) == "true":
+            
+            #if str( $gmap_options.gmap_build ) == "true":
               --gmap_build 
-              #if str($gmap_options.force_gmap_build) == "true":
+              #if str( $gmap_options.force_gmap_build ) == "true":
                   --force_gmap_build
               #end if
             #end if
-            #if str($mutation_lib_options.mutation_build) == "true":
+            
+            #if str( $mutation_lib_options.mutation_build ) == "true":
               --download_mutation_resources_url="${mutation_lib_options.source_url}" 
               --cosmic_resources_location="${mutation_lib_options.cosmic_files_location}"
-              #if str($mutation_lib_options.force_download) == "true":
+              #if str( $mutation_lib_options.force_download ) == "true":
                   --new_mutation_download
               #end if
-              #if str($mutation_lib_options.redo_integration) == "true":
+              #if str( $mutation_lib_options.redo_integration ) == "true":
                   --new_mutation_integration
               #end if
             #end if
@@ -105,6 +121,9 @@
                         <option value="same_as_download" selected="true">Build in Download location</option>
                         <option value="different_location">Build in a different location</option>
                     </param>
+                    <when value="same_as_download">
+                        <!-- do nothing here -->
+                    </when>
                     <when value="different_location">
                         <param name="different_build_location" type="text" label="Build Location (full path)" />
                     </when>