# HG changeset patch
# User ecology
# Date 1753113292 0
# Node ID 991bed85aa21b1b710c120c3074bfe7d0fa34b68
# Parent  5d257e0d5f09eeaebe122967dbda6377f7b8358b
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit bf6cd39b867fec1a8251ff9a4890f276799cdc0c

diff -r 5d257e0d5f09 -r 991bed85aa21 tool_odv.xml
--- a/tool_odv.xml	Fri Jun 13 14:11:44 2025 +0000
+++ b/tool_odv.xml	Mon Jul 21 15:54:52 2025 +0000
@@ -1,11 +1,11 @@
 <tool id="tool_odv" name="ODV collection manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
     <description>tool for qualificiation and validation</description>
     <macros>
-        <token name="@VERSION@">1.2</token>
+        <token name="@VERSION@">1.3</token>
         <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
-        <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:@VERSION@</container>
+        <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:oc@VERSION@</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export HOME=\$PWD &&
@@ -37,6 +37,7 @@
 
         /app/launchers/start-app.sh &&
         cp '/runtime/data-out/odv_collection.txt' '$output' &&
+        cp -r '/runtime/log/' './outputs/' &&
 
         cp -r '/runtime/data-out/' './outputs/'
     ]]></command>
@@ -123,7 +124,7 @@
                     <has_n_lines n="26363"/>
                 </assert_contents>
             </output>
-            <output_collection name="files" type="list" count="3"/>
+            <output_collection name="files" type="list" count="6"/>
         </test>
         <test expect_num_outputs="2">
             <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"/>
@@ -139,7 +140,7 @@
                     <has_n_lines n="17952"/>
                 </assert_contents>
             </output>
-            <output_collection name="files" type="list" count="3"/>
+            <output_collection name="files" type="list" count="6"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -157,17 +158,11 @@
 
     - file_name_raw : nc file to be qualified
     - file_name_ref : nc file used for validation / comparison. noted NULL if no files
-    - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw
-    - tool_option$subsetting : 1 apply a subbsetting to ref data searching the smallest box (default) / 0 no subsetting / -1 apply an inverse subseting
-    - tool_option$plt : figure option to see the subseted box (0 or 1) - default name subset_box.png
-
-with default values different from NULL :
-
-    - odv_collection$name : odv_collection.txt
-    - odv_collection$qc_convention : ARGO
-    - tool_action :
-    - tool_option$subsetting :
-    - tool_option$plt :
+    - operator : (optional) name of the person working on dataset qualification / validation
+    - odv_collection$name : name of the odv collection created by the tool (by default = odv_collection.txt)
+    - odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw (by default = ARGO)
+    - tool_option$subsetting : 1 apply a subsetting to ref data searching the smallest box (by default) / 0 no subsetting / -1 apply an inverse subsetting
+    - tool_option$plt : figure option to see the subsetted box (0 - by default - or 1) - default name *subset_box.png*
 
 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