# HG changeset patch
# User iuc
# Date 1770280481 0
# Node ID 2870b4cdab18b63b35528b4220cafb17027d4fc4
# Parent  a1e8960e1629e7a4259fdef28a89fc70c2d88939
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_coreprofiler commit db118f0726bf8a7d5e2c548c3e7470870accae16

diff -r a1e8960e1629 -r 2870b4cdab18 data_manager/data_manager_build_coreprofiler_download.xml
--- a/data_manager/data_manager_build_coreprofiler_download.xml	Thu Jan 08 10:29:36 2026 +0000
+++ b/data_manager/data_manager_build_coreprofiler_download.xml	Thu Feb 05 08:34:41 2026 +0000
@@ -2,7 +2,7 @@
     <description></description>
     <macros>
         <token name="@TOOL_VERSION@">2.0.0</token>
-        <token name="@VERSION_SUFFIX@">2</token>
+        <token name="@VERSION_SUFFIX@">3</token>
         <token name="@PROFILE@">22.05</token>
         <xml name="version_command">
             <version_command><![CDATA[$ coreprofiler --version]]></version_command>
@@ -47,11 +47,11 @@
 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" &&
+            source "\$PUBMLST_COREPROFILER_SECRETS_PATH" &&
         #elif $scheme_db == "bigsdb"
-            source "$BIGSDB_COREPROFILER_SECRETS_PATH" &&
+            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
+        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
@@ -71,10 +71,10 @@
         #end if
         ##
 #if $db_version == "token"
-        -k "$COREPROFILER_CONSUMER_TOKEN"
-        -ks "$COREPROFILER_CONSUMER_SECRET"
-        -a "$COREPROFILER_ACCESS_TOKEN"
-        -as "$COREPROFILER_ACCESS_SECRET"
+        -k "\$COREPROFILER_CONSUMER_TOKEN"
+        -ks "\$COREPROFILER_CONSUMER_SECRET"
+        -a "\$COREPROFILER_ACCESS_TOKEN"
+        -as "\$COREPROFILER_ACCESS_SECRET"
 #end if
 &&
 coreprofiler db makeblastdb
@@ -458,4 +458,4 @@
     <citations>
         <citation type="doi">10.3390/microorganisms10020292</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>