<tool id="damn_predict" name="dAMN Prediction Model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>dAMN Hybrid Neural Network Framework for Dynamic Flux Balance Analysis (dFBA)</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">0.1.4</token>
    </macros>
    <requirements>
        <requirement type="package" version="0.1.4">damn</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir 'figure_dir' &&
        python -m damn predict 
            --organism '$options.organism'
            --file-name '$file_name'
            --metabolite-ids
            #for $m in $options.metabolite_ids.splitlines()
                $m
            #end for
            --train-test-split '$train_test_split'
            --ods '$ods'
            --plot-type '$options.plot_type'
            --r2min '$r2min'
            --r2max '$r2max'
            --n-iter '$n_iter'
            --figure-dir 'figure_dir'
            --model-dir '$input_zip' && echo '$train_test_split' '$r2min' '$r2max' '$n_iter'
    ]]></command>
    <inputs>
        <param name="input_zip" type="data" format="zip" label="model (zip)"/>
        <conditional name="options">
            <param name='organism' type="select" label="Model Selection">
                <option value="putida" selected="true">Putida</option>
                <option value="ecoli">E.Coli</option>
                <option value="custom">Other</option>
            </param>
            <when value='putida'>
                <param name='metabolite_ids' type="text" label="Metabolite IDs" area="true" value="glc__D_e
                xyl__D_e
                succ_e
                ala__L_e
                arg__L_e
                asn__L_e
                asp__L_e
                cys__L_e
                glu__L_e
                gln__L_e
                gly_e
                his__L_e
                ile__L_e
                leu__L_e
                lys__L_e
                met__L_e
                phe__L_e
                pro__L_e
                ser__L_e
                thr__L_e
                trp__L_e
                tyr__L_e
                val__L_e
                ade_e
                gua_e
                csn_e
                ura_e
                thymd_e
                BIOMASS" help="List of metabolite IDs (Each ID on a line)"/>
                <param name='plot_type' type="select" label="Train-Test Split">
                    <option value="growth" selected="true">Growth</option>
                    <option value="substrate">Substrate</option>
                </param>
            </when>
            <when value='ecoli'>
                <param name='metabolite_ids' type="text" label="Metabolite IDs" multiple="true" value="" help="List of metabolite IDs (Each ID on a line)"/>
                <param name='plot_type' type="select" label="Train-Test Split">
                    <option value="growth">Growth</option>
                    <option value="substrate" selected="true">Substrate</option>
                </param>
            </when>
            <when value='custom'>
                <param name='metabolite_ids' type="text" label="Metabolite IDs" multiple="true" value="" help="List of metabolite IDs (Each ID on a line)"/>
                <param name='plot_type' type="select" label="Train-Test Split">
                    <option value="growth" selected="true">Growth</option>
                    <option value="substrate">Substrate</option>
                </param>
            </when>
        </conditional>
        <param name='file_name' type="text" label="File name" help="File name in the zip file (ex. 'putida_OD_81' for putida_OD_81_medium_val_ids.*) they sould all start by the same file name"/>
        <param name='train_test_split' type="select" label="Train-Test Split">
            <option value="medium" selected="true">Medium</option>
            <option value="forecast">Forecast</option>
        </param>
        <param name='ods' type="boolean" label="Biomass concentration to OD" checked="True" help="when True biomass concentration transformed in OD"/>
        <param name='r2min' type="float" label="R2 min" value="0"/>
        <param name='r2max' type="float" label="R2 max" value="0.5"/>
        <param name='n_iter' type="integer" label="Iteration num" value="3"/>
    </inputs>
    <outputs>
        <collection name="figure_col" type="list" label="Prediction plots">
            <discover_datasets pattern="(?P&lt;name&gt;.*).png" format="png" directory="figure_dir" />
        </collection>
    </outputs> 
    <tests>
        <!--python -m damn predict -organism 'putida' 
                                    -file-name 'putida_OD_81' 
                                    -metabolite-ids 'glc__D_e                 xyl__D_e                 succ_e                 ala__L_e                 arg__L_e                 asn__L_e                 asp__L_e                 cys__L_e                 glu__L_e                 gln__L_e                 gly_e                 his__L_e                 ile__L_e                 leu__L_e                 lys__L_e                 met__L_e                 phe__L_e                 pro__L_e                 ser__L_e                 thr__L_e                 trp__L_e                 tyr__L_e                 val__L_e                 ade_e                 gua_e                 csn_e                 ura_e                 thymd_e                 BIOMASS' 
                                    -train-test-split 'medium' 
                                    -ods 'true' 
                                    -plot-type 'growth' 
                                    -r2min '0.0' 
                                    -r2max '0.5' 
                                    -n-iter '3' 
                                    -figure-dir 'toto' 
                                    -model-dir 'modul.zip'-->
        <!--test prediction putida-->
        <test> 
            <param name="input_zip" value="modul.zip"/>
            <conditional name="options">
                <param name="organism" value="putida" />
            </conditional>
            <param name="file_name" value="putida_OD_81" />
            <output_collection name="figure_col" type="list" count="6"/>
        </test>
    </tests>
    
    <help><![CDATA[
dAMN Prediction
====================
dAMN Hybrid Neural Network Framework for Dynamic Flux Balance Analysis (dFBA). This tool predict using Putida ans E.Coli models add to the option of a costumed model.

**Demo data**:
---------------
`Zip Putida <https://github.com/brsynth/damn_library/blob/main/docs/putida/modul.zip>`_ (file name: putida_OD_81)

    ]]></help>
    <citations>
        <citation type="bibtex">
            @unpublished{damn_predict
                author = {Ramiz Khaled},
                title = {{damn_predict}},
                url = {https://github.com/brsynth/damn_library},
            }
        </citation>
    </citations>
</tool>