diff cads.xml @ 1:67a7303bc5c9 draft default tip

planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 7cb1c1196b3e8998743e3b4b949290e95c5d3be1

--- a/cads.xml	Sat Jun 19 18:35:50 2021 +0000
+++ b/cads.xml	Fri Mar 06 13:39:23 2026 +0000
@@ -1,22 +1,30 @@
-<tool id="cads" name="Copernicus Atmosphere Data Store" version="0.1.0" profile="20.05">
+<tool id="cads" name="Copernicus Atmosphere Data Store" version="0.1.1" profile="25.1">
     <description>for retrieving data from the Atmosphere Monitoring Service</description>
+	<edam_topics>
+      <edam_topic>topic_3855</edam_topic>
+      <edam_topic>topic_3318</edam_topic>
+    </edam_topics>
+    <edam_operations>
+      <edam_operation>operation_2422</edam_operation>
+      <edam_operation>operation_3357</edam_operation>
+      <edam_operation>operation_0335</edam_operation>
+    </edam_operations>
     <requirements>
-        <requirement type="package" version="3">python</requirement>
-        <requirement type="package" version="0.5.1">cdsapi</requirement>
-        <requirement type="package" version="1.9.9">cdo</requirement>
+		<requirement type="package" version="3.8">python</requirement>
+		<requirement type="package" version="0.7.3">cdsapi</requirement>
+		<requirement type="package" version="2.4.4">cdo</requirement>
         <requirement type="package" version="1.34">tar</requirement>
         <requirement type="package" version="6.0">unzip</requirement>
+	    <credentials name="cads_apikey" version="1.0" label="CADS API key" description="Credential for accessing Copernicus atmosphere Data Store API.">
+            <secret name="key" inject_as_env="CADS_API_KEY" optional="false" label="CADS API key" description="Your Copernicus atmosphere Data Store API key."/>
+        </credentials>
     </requirements>
-    <command detect_errors="exit_code"><![CDATA[
+	<required_files>
+        <include path="cads_retrieve.py" />
+        <include path="cads.sh" />
+    </required_files>
+	<command detect_errors="exit_code"><![CDATA[
         export HOME=`pwd`  &&
-        #set $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "")
-        #if $cads_apikey == ''
-            echo 'Error. Set your CADS credentials via: User -> Preferences -> Manage Information'  &&
-            echo 'Will try to use tool adsapirc file (used for testing)' &&
-            cp '$__tool_directory__/adsapirc.cfg' .cdsapirc &&
-        #else
-            cp '$cads_key_file' .cdsapirc &&
-        #end if
 
         python3 '$__tool_directory__/cads_retrieve.py' 
         #if str($is_file.has_req).strip() == 'yes'
@@ -29,14 +37,9 @@
         echo "Data retrieval from Copernicus Atmosphere Data Store is done"
     ]]></command>
     <configfiles>
-        <configfile name="cads_key_file"><![CDATA[
-#set $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "")
-         url: https://ads.atmosphere.copernicus.eu/api/v2
-         key: $cads_apikey
-        ]]></configfile>
         <configfile name="req_from_paste"><![CDATA[
        #if str($is_file.has_req).strip() == 'no'
-$is_file.api_req_text
+			$is_file.api_req_text
        #end if
         ]]></configfile>
     </configfiles>
@@ -55,25 +58,27 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="request" format="txt" from_work_dir="request.txt"/>
-        <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>
+        <data name="request" format="txt" from_work_dir="request.txt" label="Request"/>
+        <data name="filename" format="netcdf" from_work_dir="tmp.nc" label="Netcdf file"/>
     </outputs>
     <tests>
-        <test>
+        <test expect_failure="true">
             <conditional name="is_file">
                 <param name="has_req" value="yes" />
                 <param name="api_req_file" ftype="txt" value="req.txt" />
             </conditional>
-            <output name="request" value="req_out.txt" compare="sim_size" delta="10"/>
-            <output name="ofilename" ftype="netcdf" value="output.nc" compare="sim_size" delta="100"/>
+            <assert_stderr>
+                <has_text text="CADS retrieval failed, make sure you filled in your CADS API Key"/>
+            </assert_stderr>
         </test>
-        <test>
+        <test expect_failure="true">
             <conditional name="is_file">
                 <param name="has_req" value="yes" />
                 <param name="api_req_file" ftype="txt" value="req-timeseries.txt" />
             </conditional>
-            <output name="request" value="timeseries_out.txt" compare="sim_size" delta="10"/>
-            <output name="ofilename" ftype="netcdf" value="timeseries.nc" compare="sim_size" delta="100"/>
+            <assert_stderr>
+                <has_text text="CADS retrieval failed, make sure you filled in your CADS API Key"/>
+            </assert_stderr>
         </test>
     </tests>
     <help><![CDATA[
@@ -84,10 +89,10 @@
 This tool is a wrapper to retrieve data from the Copernicus Atmosphere Data Store.
 
 - It allows to retrieve data from the Copernicus Atmosphere Monitoring Service.
-- Any user willing to use this tool needs to `create a new account <https://ads.atmosphere.copernicus.eu/user/register?destination=/api-how-to|>`_.
-- Set your CADS API Key via: User -> Preferences -> Manage Information"
-- Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/api-how-to>`_.
-- Compose your request directly on Copernicus Atmosphere Data Store and copy/paste it in the input field "Request" or save it in a file.
+- Any user willing to use this tool needs to `create a new account here <https://ads.atmosphere.copernicus.eu/>`_.
+- Set your CADS API Key in the credentials
+- Your CADS API key can be found `here <https://ads.atmosphere.copernicus.eu/profile>`_.
+- Compose your request directly on Copernicus Atmosphere Data Store and copy/paste it in the input field "Request" or save it in a file mor information on how to proceed in the `documentation <https://ads.atmosphere.copernicus.eu/user-guide>` .
 - Be aware that for being able to download dataset from ADS, users also need to agree to their term of use (Licence to use Copernicus Products) on the ADS website.
 
 License:
@@ -98,14 +103,6 @@
 that may be made of the Copernicus information or data it contains.
     ]]></help>
     <citations>
+	    <citation type="bibtex">@misc{CADS,author={Copernicus Atmosphere Data Store}}</citation>
     </citations>
-    <edam_topics>
-      <edam_topic>topic_3855</edam_topic>
-      <edam_topic>topic_3318</edam_topic>
-    </edam_topics>
-    <edam_operations>
-      <edam_operation>operation_2422</edam_operation>
-      <edam_operation>operation_3357</edam_operation>
-      <edam_operation>operation_0335</edam_operation>
-    </edam_operations>
 </tool>