# HG changeset patch
# User iuc
# Date 1770376138 0
# Node ID adc9ab7a10abb6ca6991ce2ff9d60d554c01cc97
# Parent  99fe0ae4e5862389a0b39ab45622ecebbee058fe
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit d4c7bfd623ecf2599435c71353052359a5ec63d2

diff -r 99fe0ae4e586 -r adc9ab7a10ab data_manager/data_manager_build_coreprofiler_download.xml
--- a/data_manager/data_manager_build_coreprofiler_download.xml	Thu Feb 05 08:34:51 2026 +0000
+++ b/data_manager/data_manager_build_coreprofiler_download.xml	Fri Feb 06 11:08:58 2026 +0000
@@ -2,7 +2,7 @@
     <description></description>
     <macros>
         <token name="@TOOL_VERSION@">2.0.0</token>
-        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@VERSION_SUFFIX@">4</token>
         <token name="@PROFILE@">22.05</token>
         <xml name="version_command">
             <version_command><![CDATA[$ coreprofiler --version]]></version_command>
@@ -44,7 +44,7 @@
 #end if
 
 mkdir -p '$out_file.extra_files_path' &&
-mkdir -p coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name/ &&
+mkdir -p 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name/' &&
 #if $db_version == "token"
         #if $scheme_db == "pubmlst"
             source "\$PUBMLST_COREPROFILER_SECRETS_PATH" &&
@@ -52,21 +52,22 @@
             source "\$BIGSDB_COREPROFILER_SECRETS_PATH" &&
         #end if
         if [[ -z "\$COREPROFILER_CONSUMER_TOKEN" || -z "\$COREPROFILER_CONSUMER_SECRET" || -z "\$COREPROFILER_ACCESS_TOKEN" || -z "\$COREPROFILER_ACCESS_SECRET" ]]; then
-            echo "Error: Missing required bash variables for CoreProfiler authentication." >&2
-            echo "Please set the following variables before running this tool:" >&2
-            echo "  COREPROFILER_CONSUMER_TOKEN" >&2
-            echo "  COREPROFILER_CONSUMER_SECRET" >&2
-            echo "  COREPROFILER_ACCESS_TOKEN" >&2
-            echo "  COREPROFILER_ACCESS_SECRET" >&2
-            echo "Please refer to the data manager help section for more information on how to generate these tokens." >&2
-        fi &&
+            echo "Error: Missing required bash variables for CoreProfiler authentication." >&2 ;
+            echo "Please set the following variables before running this tool:" >&2 ;
+            echo "  COREPROFILER_CONSUMER_TOKEN" >&2 ;
+            echo "  COREPROFILER_CONSUMER_SECRET" >&2 ;
+            echo "  COREPROFILER_ACCESS_TOKEN" >&2 ;
+            echo "  COREPROFILER_ACCESS_SECRET" >&2 ;
+            echo "Please refer to the data manager help section for more information on how to generate these tokens." >&2 ;
+            exit 1;
+        fi ;
 #end if
 
     coreprofiler db download 
-        -s $scheme_name
-        -o coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name
+        -s '$scheme_name'
+        -o 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name'
         ## Used only for test 
-        #if str($hide_test) == 'true':
+        #if $hide_test
             -t
         #end if
         ##
@@ -78,11 +79,11 @@
 #end if
 &&
 coreprofiler db makeblastdb
-    -s coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name 
-    -n $scheme_name 
-    -p coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/db_$scheme_name &&
+    -s 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/scheme_$scheme_name'
+    -n '$scheme_name'
+    -p 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}/db_$scheme_name' &&
 
-mv coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today} '$out_file.extra_files_path' &&
+mv 'coreprofiler_${scheme_name}_${scheme_db}_${db_version}_${today}' '$out_file.extra_files_path' &&
 
 cp '$dmjson' '$out_file'
     ]]></command>