<tool id="fluxSampling" name="COBRAxy Model sampling" version="2.0.0">
    
    <macros>
        <import>marea_macros.xml</import>
    </macros>

	<requirements>
        <requirement type="package" version="0.29.0">cobra</requirement>
        <requirement type="package" version="4.9.3">lxml</requirement>
	</requirements>

    <command detect_errors="exit_code">
        <![CDATA[
      	python $__tool_directory__/flux_sampling.py
        --input $input
        --name $input.element_identifier
        #if $algorithm_param.algorithm == 'OPTGP':
        	--thinning $thinning
        --n_batches $n_batches
        --n_samples $n_samples
        --seed $seed
        --output_format $output_format
        --out_log $log
        ]]>
    </command>
    <inputs>
        <param name="input" argument="--input" type="data" format="xml, json" label="Model:" />

        <conditional name="algorithm_param">
			<param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:">
                    <option value="CBS" selected="true">CBS</option>
                	<option value="OPTGP">OPTGP</option>
        	</param>
        	<when value="OPTGP">
        		<param name="thinning" argument="--thinning" type="integer" label="Thinning:" />
        	</when>

		</conditional>

        <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" default="1"/>

        <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" default="1000"/>

        <param name="seed" argument="--seed" type="integer" label="Seed:" default="0"/>
        
        <param name="output_format" argument="--output_format" type="select" label="Output files format:">
            <option value="p" selected="true">pickle extension (binary, non-editable, pre-parsed)</option>
            <option value="csv">Comma Separated Values (csv text file, editable, raw)</option>
        </param>
    </inputs>

    <outputs>
        <data format="txt" name="log" label="fluxSampling - $name - Log" />
        
        <collection name="results" type="list" label="Model sampling result ($output_format)">
            <discover_datasets name = "collection" pattern="__name_and_ext__" directory="result"/>
        </collection>
    </outputs>

    <help>
    <![CDATA[
What it does
-------------

This tool generates feasible samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) and OPTGP (mproved Artificial Centering Hit-and-Run sampler) sampling algorithms.

Accepted files:
    - A model: JSON or XML file reporting reactions and rules contained in the model.   


Output:
-------------

The tool generates:
    - Samples: reporting the sampled fluxes for each reaction in the custom model given. Format: csv or pickle.
    - a log file (.txt).
    ]]>
    </help>
    <expand macro="citations" />
</tool>