Mercurial > repos > climate > cads

annotate cads.xml @ 0:b768e517a7d0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
author climate
date Sat, 19 Jun 2021 18:35:50 +0000
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
climate
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1 <tool id="cads" name="Copernicus Atmosphere Data Store" version="0.1.0" profile="20.05">
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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2 <description>for retrieving data from the Atmosphere Monitoring Service</description>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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3 <requirements>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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4 <requirement type="package" version="3">python</requirement>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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5 <requirement type="package" version="0.5.1">cdsapi</requirement>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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6 <requirement type="package" version="1.9.9">cdo</requirement>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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7 <requirement type="package" version="1.34">tar</requirement>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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8 <requirement type="package" version="6.0">unzip</requirement>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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9 </requirements>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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10 <command detect_errors="exit_code"><![CDATA[
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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11 export HOME=`pwd` &&
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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12 #set $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "")
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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13 #if $cads_apikey == ''
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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14 echo 'Error. Set your CADS credentials via: User -> Preferences -> Manage Information' &&
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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15 echo 'Will try to use tool adsapirc file (used for testing)' &&
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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16 cp '$__tool_directory__/adsapirc.cfg' .cdsapirc &&
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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17 #else
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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18 cp '$cads_key_file' .cdsapirc &&
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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19 #end if
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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20
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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21 python3 '$__tool_directory__/cads_retrieve.py'
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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22 #if str($is_file.has_req).strip() == 'yes'
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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23 --request '$is_file.api_req_file'
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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24 #else
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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25 --request '$req_from_paste'
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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26 #end if
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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27 --output request.txt &&
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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28 bash '$__tool_directory__/cads.sh' &&
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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29 echo "Data retrieval from Copernicus Atmosphere Data Store is done"
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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30 ]]></command>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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31 <configfiles>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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32 <configfile name="cads_key_file"><![CDATA[
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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33 #set $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "")
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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34 url: https://ads.atmosphere.copernicus.eu/api/v2
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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35 key: $cads_apikey
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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36 ]]></configfile>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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37 <configfile name="req_from_paste"><![CDATA[
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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38 #if str($is_file.has_req).strip() == 'no'
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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39 $is_file.api_req_text
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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40 #end if
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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41 ]]></configfile>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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42 </configfiles>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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43 <inputs>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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44 <conditional name="is_file">
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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45 <param name="has_req" type="select" label="Provide CADS request">
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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46 <option value="no">paste as text</option>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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47 <option value="yes" selected="true">give a filename</option>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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48 </param>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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49 <when value="yes">
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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50 <param name="api_req_file" type="data" label="API Request filename" format="txt"/>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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51 </when>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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52 <when value="no">
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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53 <param name="api_req_text" type="text" label="Paste API Request" area="true" />
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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54 </when>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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55 </conditional>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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56 </inputs>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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57 <outputs>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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58 <data name="request" format="txt" from_work_dir="request.txt"/>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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59 <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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60 </outputs>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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61 <tests>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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62 <test>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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63 <conditional name="is_file">
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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64 <param name="has_req" value="yes" />
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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65 <param name="api_req_file" ftype="txt" value="req.txt" />
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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66 </conditional>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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67 <output name="request" value="req_out.txt" compare="sim_size" delta="10"/>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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68 <output name="ofilename" ftype="netcdf" value="output.nc" compare="sim_size" delta="100"/>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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69 </test>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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70 <test>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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71 <conditional name="is_file">
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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72 <param name="has_req" value="yes" />
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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73 <param name="api_req_file" ftype="txt" value="req-timeseries.txt" />
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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74 </conditional>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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75 <output name="request" value="timeseries_out.txt" compare="sim_size" delta="10"/>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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76 <output name="ofilename" ftype="netcdf" value="timeseries.nc" compare="sim_size" delta="100"/>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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77 </test>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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78 </tests>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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79 <help><![CDATA[
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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80
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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81 **Copernicus Atmosphere Data Store (ADS)**
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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82 =======================================================================================================
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83
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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84 This tool is a wrapper to retrieve data from the Copernicus Atmosphere Data Store.
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85
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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86 - It allows to retrieve data from the Copernicus Atmosphere Monitoring Service.
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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87 - Any user willing to use this tool needs to `create a new account <https://ads.atmosphere.copernicus.eu/user/register?destination=/api-how-to|>`_.
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88 - Set your CADS API Key via: User -> Preferences -> Manage Information"
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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89 - Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/api-how-to>`_.
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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90 - Compose your request directly on Copernicus Atmosphere Data Store and copy/paste it in the input field "Request" or save it in a file.
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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91 - 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.
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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92
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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93 License:
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94 ~~~~~~~~
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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95
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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96 Generated using Copernicus Atmosphere Monitoring Service information [2021]
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97 Neither the European Commission nor ECMWF is responsible for any use
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98 that may be made of the Copernicus information or data it contains.
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99 ]]></help>
b768e517a7d0 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
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100 <citations>
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101 </citations>
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102 <edam_topics>
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103 <edam_topic>topic_3855</edam_topic>
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104 <edam_topic>topic_3318</edam_topic>
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105 </edam_topics>
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106 <edam_operations>
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107 <edam_operation>operation_2422</edam_operation>
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108 <edam_operation>operation_3357</edam_operation>
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109 <edam_operation>operation_0335</edam_operation>
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110 </edam_operations>
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111 </tool>