# HG changeset patch
# User ecology
# Date 1742482198 0
# Node ID 87ae77f2bd5ae461554b3f17880dd17351975841
# Parent c07f11d8e49a1b9c5e053f409b66c20e4d379052
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean commit ecc01d1975d2a603ece634c6cfe2d9591b307cc8
diff -r c07f11d8e49a -r 87ae77f2bd5a check.py
--- a/check.py Mon Nov 18 10:39:18 2024 +0000
+++ b/check.py Thu Mar 20 14:49:58 2025 +0000
@@ -76,6 +76,10 @@
print(error_message)
sys.exit(1)
+ # Append '--force-download' option to the command
+ if "--force-download" not in command:
+ command += " --force-download"
+
# Execute the command
try:
subprocess.run(command, shell=True, check=True)
diff -r c07f11d8e49a -r 87ae77f2bd5a copernicusmarine.xml
--- a/copernicusmarine.xml Mon Nov 18 10:39:18 2024 +0000
+++ b/copernicusmarine.xml Thu Mar 20 14:49:58 2025 +0000
@@ -2,45 +2,28 @@
retrieve marine data
1.3.3
- 1
+ 2
copernicusmarine
Preferences -> Manage Information' &&
- #end if
+ bash '$cmems_credentials' &&
- #set $filename="config_file_with_my_command"
- echo -e '$input_text' > $filename --force-download --username $cmems_username --password $cmems_password &&
-
- python '$__tool_directory__/check.py' $filename
+ echo -e '$input_text' > config_file_with_my_command &&
+ python '$__tool_directory__/check.py' 'config_file_with_my_command'
]]>
- #set $cmems_username = $__user__.extra_preferences.get('cmems_username', "")
- #set $cmems_password = $__user__.extra_preferences.get('cmems_password', "")
- cmems_username: $cmems_username
- cmems_password: $cmems_password
+#import os
+#set $cmems_username = $__user__.extra_preferences.get('cmems_username', "")
+#set $cmems_password = $__user__.extra_preferences.get('cmems_password', "")
+#if $cmems_username == "" or $cmems_password == ""
+ #set $cmems_username = os.getenv('CMEMS_USERNAME', '')
+ #set $cmems_password = os.getenv('CMEMS_PASSWORD', '')
+#end if
+export cmems_username='$cmems_username'
+export cmems_password='$cmems_password'