Mercurial > repos > ecology > tool_odv_history

changeset 4:94c2de92bccc draft

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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 15:54:45 +0000
parents 9e462c4e8367
children 2c592f49814d
files tool_odv_history.xml
diffstat 1 files changed, 13 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/tool_odv_history.xml	Fri Jun 13 14:11:38 2025 +0000
+++ b/tool_odv_history.xml	Mon Jul 21 15:54:45 2025 +0000
@@ -1,11 +1,11 @@
 <tool id="tool_odv_history" name="ODV history manager" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05" license="MIT">
     <description>reports user action performed with ODV</description>
     <macros>
-        <token name="@VERSION@">1.1</token>
+        <token name="@VERSION@">1.2</token>
         <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
-        <container type="docker">easyqcvbgc/easy-qcv_odv-history-manager_tool:@VERSION@</container>
+        <container type="docker">easyqcvbgc/easy-qcv_odv-history-manager_tool:oh@VERSION@</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export HOME=\$PWD &&
@@ -38,7 +38,7 @@
         #end if 
 
         /app/launchers/start-app.sh &&
-        ###cp '/runtime/data-out/*data_0_qced.nc' '$output' &&
+        cp -r '/runtime/log/' './outputs/' &&
 
         cp -r '/runtime/data-out/' './outputs/'
     ]]></command>
@@ -78,7 +78,7 @@
         </configfile>
     </configfiles>
     <inputs>
-        <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input netcdf data" help="This netcdf should come from the QCV harmonizer tool"/>
+        <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input netcdf data" help="This netcdf should come from the QCV harmonizer tool or the BioGeoChemical calibration tool "/>
         <param name="input_hist" type="data" format="txt" multiple="true" label="Input history text file" help="This text file should be the history extracted from the Ocean Data View (ODV) tool"/>
         <param name="input_odv" type="data" format="txt" multiple="true" optional="true" label="Input odv file" help="This ODV file should be the odv_collection.txt from the ODV collection manager tool."/>
         <conditional name="config">
@@ -120,9 +120,12 @@
         <collection type="list" name="csv_files" label="ODV history manager csv collection">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.csv" directory="./outputs" recurse="true" format="csv"/>
         </collection>
+        <collection type="list" name="log_files" label="ODV history manager log files">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.log" directory="./outputs" recurse="true" format="txt"/>
+        </collection>
     </outputs>
     <tests>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/QCV_harmonizer_NetCDF_data_0.nc"/>
             <param name="input_hist" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/history_from_odv_collection.txt"/>
             <param name="input_odv" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/odv_collection.txt"/>
@@ -131,8 +134,9 @@
             </conditional>
             <output_collection name="nc_files" type="list" count="1"/>
             <output_collection name="csv_files" type="list" count="1"/>
+            <output_collection name="log_files" type="list" count="3"/>
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="input_raw" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/QCV_harmonizer_NetCDF_data_0.nc"/>
             <param name="input_hist" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/history_from_odv_collection.txt"/>
             <param name="input_odv" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-bgc-tools/-/raw/fe047f301f0c384ad0668a73dfe776d9ac482d0f/galaxy_tool/test-data/odv_collection.txt"/>
@@ -143,6 +147,7 @@
             </conditional>
             <output_collection name="nc_files" type="list" count="1"/>
             <output_collection name="csv_files" type="list" count="1"/>
+            <output_collection name="log_files" type="list" count="3"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -152,12 +157,11 @@
 
 **What it does**
 
-This tool present two type of actions :
-    - history : the tool report in the input file the ODV history including the change of QC flag 
+This tool reports in the input file (a netcdf from the QCV harmonizer tool or the BioGeoChemical calibration tool) the ODV history including the change of QC flag.
 
 **Input description**
 
-    file_name_raw : nc file to be qualified
+    file_name_raw : nc file to be qualified, this netcdf should come from the QCV harmonizer tool or  from the BioGeoChemical calibration tool 
     file_name_history : history txt file extracted from ODV (manualy or automatically)
     odv_collection$name : name of the odv collection view with webODV and updated
     odv_collection$qc_convention : tool makes mapping when its necessary and when global attribute qc_convention is available and filled in file_name_raw