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comparison tool_odv.xml @ 5:991bed85aa21 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit bf6cd39b867fec1a8251ff9a4890f276799cdc0c
author ecology
date Mon, 21 Jul 2025 15:54:52 +0000
parents 5d257e0d5f09
children
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4:5d257e0d5f09 5:991bed85aa21
1 <tool id="tool_odv" name="ODV collection manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT"> 1 <tool id="tool_odv" name="ODV collection manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
2 <description>tool for qualificiation and validation</description> 2 <description>tool for qualificiation and validation</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">1.2</token> 4 <token name="@VERSION@">1.3</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:@VERSION@</container> 8 <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:oc@VERSION@</container>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 export HOME=\$PWD && 11 export HOME=\$PWD &&
12 mkdir -p /runtime/config && 12 mkdir -p /runtime/config &&
13 mkdir -p '/runtime/data-in-raw/' && 13 mkdir -p '/runtime/data-in-raw/' &&
35 cp '${config_file}' '/runtime/config/config_user_odv_tool.yml' && 35 cp '${config_file}' '/runtime/config/config_user_odv_tool.yml' &&
36 #end if 36 #end if
37 37
38 /app/launchers/start-app.sh && 38 /app/launchers/start-app.sh &&
39 cp '/runtime/data-out/odv_collection.txt' '$output' && 39 cp '/runtime/data-out/odv_collection.txt' '$output' &&
40 cp -r '/runtime/log/' './outputs/' &&
40 41
41 cp -r '/runtime/data-out/' './outputs/' 42 cp -r '/runtime/data-out/' './outputs/'
42 ]]></command> 43 ]]></command>
43 <configfiles> 44 <configfiles>
44 <configfile name="config_file"> 45 <configfile name="config_file">
121 <output name="output"> 122 <output name="output">
122 <assert_contents> 123 <assert_contents>
123 <has_n_lines n="26363"/> 124 <has_n_lines n="26363"/>
124 </assert_contents> 125 </assert_contents>
125 </output> 126 </output>
126 <output_collection name="files" type="list" count="3"/> 127 <output_collection name="files" type="list" count="6"/>
127 </test> 128 </test>
128 <test expect_num_outputs="2"> 129 <test expect_num_outputs="2">
129 <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool/-/raw/7b3557c89438b7347c601d6959af354103b167a1/galaxy_tool/test-data/data_raw.nc"/> 130 <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool/-/raw/7b3557c89438b7347c601d6959af354103b167a1/galaxy_tool/test-data/data_raw.nc"/>
130 <conditional name="config"> 131 <conditional name="config">
131 <param name="type" value="yes"/> 132 <param name="type" value="yes"/>
137 <output name="output"> 138 <output name="output">
138 <assert_contents> 139 <assert_contents>
139 <has_n_lines n="17952"/> 140 <has_n_lines n="17952"/>
140 </assert_contents> 141 </assert_contents>
141 </output> 142 </output>
142 <output_collection name="files" type="list" count="3"/> 143 <output_collection name="files" type="list" count="6"/>
143 </test> 144 </test>
144 </tests> 145 </tests>
145 <help><![CDATA[ 146 <help><![CDATA[
146 ====================== 147 ======================
147 ODV collection manager 148 ODV collection manager
155 156
156 **Input description** 157 **Input description**
157 158
158 - file_name_raw : nc file to be qualified 159 - file_name_raw : nc file to be qualified
159 - file_name_ref : nc file used for validation / comparison. noted NULL if no files 160 - file_name_ref : nc file used for validation / comparison. noted NULL if no files
160 - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw 161 - operator : (optional) name of the person working on dataset qualification / validation
161 - tool_option$subsetting : 1 apply a subbsetting to ref data searching the smallest box (default) / 0 no subsetting / -1 apply an inverse subseting 162 - odv_collection$name : name of the odv collection created by the tool (by default = odv_collection.txt)
162 - tool_option$plt : figure option to see the subseted box (0 or 1) - default name subset_box.png 163 - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw (by default = ARGO)
163 164 - tool_option$subsetting : 1 apply a subsetting to ref data searching the smallest box (by default) / 0 no subsetting / -1 apply an inverse subsetting
164 with default values different from NULL : 165 - tool_option$plt : figure option to see the subsetted box (0 - by default - or 1) - default name *subset_box.png*
165
166 - odv_collection$name : odv_collection.txt
167 - odv_collection$qc_convention : ARGO
168 - tool_action :
169 - tool_option$subsetting :
170 - tool_option$plt :
171 166
172 If the list of raw file name is empty, tool stops If the user make an error in the file extension, tool changes it by itself. If the user miss the yaml configuration, tool uses its default config and upload file in data-in-raw and data-in-ref 167 If the list of raw file name is empty, tool stops If the user make an error in the file extension, tool changes it by itself. If the user miss the yaml configuration, tool uses its default config and upload file in data-in-raw and data-in-ref
173 168
174 **Output** 169 **Output**
175 170