<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_SUFFIX@">1</token>
    </macros>
    <requirements>
        <container type="docker">easyqcvbgc/easy-qcv_odv-coll-manager_tool:@VERSION@</container>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        export HOME=\$PWD &&
        mkdir -p /runtime/config &&
        mkdir -p '/runtime/data-in-raw/' &&
        mkdir -p '/runtime/data-in-ref/' &&
        mkdir -p '/runtime/data-out/' &&
        mkdir -p ./outputs &&

	#for $i, $infile in enumerate($input_raw):
            #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}' &&
            #end for
        #end if
        
        #if $config.type == 'yes':
            ## Write YAML content
            cp '${config_file}' '/runtime/config/config_user_odv_tool.yml' &&
        #end if 

        /app/launchers/start-app.sh &&
        cp '/runtime/data-out/odv_collection.txt' '$output' &&

        cp -r '/runtime/data-out/' './outputs/'
    ]]></command>
    <configfiles>
        <configfile name="config_file">
        #if $config.type == 'yes':
                default:
                    file_name_list_raw: 
                        #for $i, $infile in enumerate($input_raw):
                            #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 
                        #end for
                        - ${name_raw}
                    operator: '${config.operator}' 
                QV:
                    file_name_list_ref: 
                        #for $i, $infile in enumerate($input_ref):
                            #set name_ref='${infile.element_identifier}'
                        #end for
                        - ${name_ref}
                    odv_collection:
                        name: "odv_collection.txt"
                        qc_convention: '${config.qc_convention}' 
                    tool_option:
                        subsetting: '${config.subsetting}' 
                        plt: '${config.plt}' 
        #end if 
        </configfile>
    </configfiles>
    <inputs>
        <param name="input_raw" type="data" format="netcdf" multiple="true" label="Input raw data"/>
        <param name="input_ref" type="data" format="netcdf" multiple="true" optional="true" label="Input reference data"/>
        <conditional name="config">
            <param name="type" type="select" label="Select if you want to write your own configuration file or not.">   
                <option value="no">No, I don't want to, I'll use the default one</option>
                <option value="yes">Yes, I to write my own configuration file</option>
            </param>
            <when value="yes">
                <param name="operator" type="text" value="Anonymous" label="Enter operator name"/>
                <param name="qc_convention" type="select" label="Enter QC convention for the ODV collection output (default: ARGO)">
                    <option value="ARGO">ARGO</option>
                    <option value="ODV">ODV</option>
                    <option value="GTSPP">GTSPP</option>
                    <option value="SEADATANET">SEADATANET</option>
                    <option value="ESEAS">ESEAS</option>
                    <option value="WOD">WOD</option>
                    <option value="WODSTATION">WODSTATION</option>
                    <option value="WOCEBOTTLE">WOCEBOTTLE</option>
                    <option value="WOCECTD">WOCECTD</option>
                    <option value="QARTOD">QARTOD</option>
                    <option value="BODC">BODC</option>
                    <option value="PANGAEA">PANGAEA</option>
                    <option value="SMHI">SMHI</option>
                    <option value="OceanSITES">OceanSITES</option>
                    <option value="IODE">IODE</option>
                </param>
                <param name="subsetting" type="float" min="-1" max="1" value="1" label="Enter subsetting (default: 1)"/>
                <param name="plt" type="float" min="0" max="1" value="0" label="Enter plt (default: 0 for QV, 1 for demo)"/>
            </when>
            <when value="no">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="ODV tool output"/>
        <collection type="list" name="files" label="ODV tool collection">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="./outputs" recurse="true" format="txt"/>
        </collection>
    </outputs>
    <tests>
        <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"/>
            <param name="input_ref" location="https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool/-/raw/7b3557c89438b7347c601d6959af354103b167a1/galaxy_tool/test-data/data_ref.nc"/>
            <conditional name="config">
                <param name="type" value="no"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_n_lines n="26363"/>
                </assert_contents>
            </output>
            <output_collection name="files" type="list" count="3"/>
        </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"/>
            <conditional name="config">
                <param name="type" value="yes"/>
                <param name="operator" value="anonymous"/>
                <param name="qc_convention" value="ARGO"/>
                <param name="subsetting" value="1"/>
                <param name="plt" value="0"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_n_lines n="17952"/>
                </assert_contents>
            </output>
            <output_collection name="files" type="list" count="3"/>
        </test>
    </tests>
    <help><![CDATA[
======================
ODV collection manager
======================

**What it does**

This tool present two type of actions :

    - 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.

**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 :

    - 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, 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

**Output**

This tool creates a single generic ODV spreadsheet following ODV user’s guide 

    ]]></help>
    <citations>
        <citation type="bibtex">
            @Manual{,
            title = {ODV tool},
            author = {Pokapok},
            year = {2024},
            note = {https://gitlab.com/pokapok-projects/easy-qcv-bgc/qcv-odv-tool}
        </citation>    
    </citations>
</tool>