# HG changeset patch
# User ecology
# Date 1749823901 0
# Node ID 689d7a46e3594671bc051ee03ad3b64185dfd35c
# Parent  6f66f964d64c667a5d81532ddaf47b18c4751d41
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean_data_view_manager commit 03e7755bd0554044c4ca46c27007ee03a58b8d89

diff -r 6f66f964d64c -r 689d7a46e359 bgc_calib.xml
--- a/bgc_calib.xml	Wed Jun 11 18:23:33 2025 +0000
+++ b/bgc_calib.xml	Fri Jun 13 14:11:41 2025 +0000
@@ -2,7 +2,7 @@
     <description>for sensors according to Argo recommendations</description>
     <macros>
         <token name="@VERSION@">1.0</token>
-        <token name="@VERSION_SUFFIX@">0.1</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <container type="docker">easyqcvbgc/easy-qcv_calibration-methods_tool:@VERSION@</container>
@@ -16,8 +16,14 @@
         mkdir -p ./outputs &&
 
 	#for $i, $infile in enumerate($input_raw):
-            cp '$infile' '/runtime/data-in-raw/${infile.element_identifier}.nc' &&
-        #end for	
+            #set real_name = $infile.element_identifier
+            #set extension = $real_name.split('.')[-1]
+            #if  $extension == 'nc':
+                cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}" &&
+            #else
+                cp '${infile.file_name}' "/runtime/data-in-raw/${infile.element_identifier}.nc" &&
+            #end if
+	#end for	
         #if $input_ref:
             #for $i, $infile in enumerate($input_ref):            
             	cp '$infile' '/runtime/data-in-ref/${infile.element_identifier}' &&
@@ -41,7 +47,13 @@
                 default :
                     file_name_list_raw:
                         #for $i, $infile in enumerate($input_raw):
-                            #set name_raw='${infile.element_identifier}.nc'
+                            #set real_name = $infile.element_identifier
+                            #set extension = $real_name.split('.')[-1]
+                            #if  $extension == 'nc':
+                                #set name_raw='${infile.element_identifier}'
+                            #else:
+                                #set name_raw='${infile.element_identifier}.nc'
+                            #end if 
                             - ${name_raw}  
                         #end for
                     param : nitrate
@@ -50,7 +62,7 @@
                         to_be_replaced : '${param_qc_toreplaced}'
                         replaced_by : '${param_qc_replacedby}'
                     calib_configs :
-                        - number : 1  
+                        - number : '${i}'
                             method_raw : 
                                 name : method1
                                 options : 
@@ -198,37 +210,43 @@
         </test>
     </tests>
     <help><![CDATA[
-======================
-ODV collection manager
-======================
+==========================
+BioGeoChemical calibration
+==========================
 
 **What it does**
 
-This tool present two type of actions :
+This tool calibrates BioGeoChemical (BGC) data measured by ARGO or GLIDER network. The BGC variables managed by the tool for the moment are :
 
-    - qualificiation & validation : the tool merges various datasets with a common vocabulary and creates a single generic ODV spreadsheet following ODV user’s guide (v5.7.0) in an automatic way.
+- NITRATE using methods published in `archimer <https://archimer.ifremer.fr/doc/00350/46121/>`
+
 
 **Input description**
 
-    - 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$plt : figure option to see the subseted box (0 or 1) - default name subset_box.png
-
-with default values different from NULL :
+- file_name_raw : nc file to be qualified
+- param_qc$bad : qc values to be removed from param before calibration
+- param_qc$to_be_replaced : raw qc values to be replaced for building the adjusted qc values
+- param_qc$replaced_by : good qc value replacing raw qc values for building adjusted qc values
+- method_raw$name which method/equation will be used for estimating the adjusted variable
+- method_raw$options :
+	- bypass_P : 0 (tool defines the P of reference for adjustment ) OR 1 (user defines P and chooses P below)
+        - P : NULL (if bypass_P = 0) OR numeric_values (if bypass_P = 1)
+        - multiple_linear_regression : 0 (automatic choice of N) or 1 (single linear regression) or N>1 (N linear regressions)
+        - single_favored : FALSE or TRUE to favored the single linear regression
+- method_ref$name : which kind of reference method (for example model or climatology) will be used by the method_raw for estimating the adjusted variable.
+- reference : which reference method like canyonb or woa will be used by the method_raw for estimating the adjusted variable.
 
-    - odv_collection$name : odv_collection.txt
-    - odv_collection$qc_convention : ARGO
-    - tool_action :
-    - tool_option$subsetting :
-    - tool_option$plt :
+If the list of raw file name is empty, the tool stops If the user makes an error in the file extension, tool changes it by itself. If the user misses the yaml configuration, tool uses its default config and upload available files in data-in-raw
+
+compatibility matrix
 
-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
-
+- variable / application mode / [method_raw.name, method_ref.name, reference]
+- nitrate / R_APP_CN / [method1, model, canyon_b] & [method1, model, canyon_med] & [method1, clim, woa]
+	    
 **Output**
 
-This tool creates a single generic ODV spreadsheet following ODV user’s guide 
+- an extended nc file including the _adjusted and _adjusted_qc
+- figures helping to understand the adjustment
 
     ]]></help>
     <citations>