diff cads.xml @ 0:b768e517a7d0 draft default tip

"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cads.xml	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,111 @@
+<tool id="cads" name="Copernicus Atmosphere Data Store" version="0.1.0" profile="20.05">
+    <description>for retrieving data from the Atmosphere Monitoring Service</description>
+    <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="1.34">tar</requirement>
+        <requirement type="package" version="6.0">unzip</requirement>
+    </requirements>
+    <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($is_file.has_req).strip() == 'yes'
+            --request '$is_file.api_req_file' 
+        #else
+            --request '$req_from_paste'
+        #end if
+        --output request.txt &&
+        bash '$__tool_directory__/cads.sh' &&
+        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
+       #end if
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <conditional name="is_file">
+            <param name="has_req" type="select" label="Provide CADS request">
+                <option value="no">paste as text</option>
+                <option value="yes" selected="true">give a filename</option>
+            </param>
+            <when value="yes">
+                <param name="api_req_file" type="data" label="API Request filename" format="txt"/>
+            </when>
+            <when value="no">
+                <param name="api_req_text" type="text" label="Paste API Request" area="true" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="request" format="txt" from_work_dir="request.txt"/>
+        <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>
+    </outputs>
+    <tests>
+        <test>
+            <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"/>
+        </test>
+        <test>
+            <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"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**Copernicus Atmosphere Data Store (ADS)**
+=======================================================================================================
+
+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.
+- 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:
+~~~~~~~~
+
+Generated using Copernicus Atmosphere Monitoring Service information [2021]
+Neither the European Commission nor ECMWF is responsible for any use 
+that may be made of the Copernicus information or data it contains.
+    ]]></help>
+    <citations>
+    </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>