view marea_2_0/model_generator.xml @ 225:0952b16a7ef9 draft

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<tool id="modelGenerator" name="COBRAxy Model generator" 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>
        <requirement type="package" version="1.4.2">joblib</requirement>
	</requirements>

    <command detect_errors="exit_code">
        <![CDATA[
        python $__tool_directory__/model_generator.py
        --model_selector $cond_model.model_selector
        --tool_dir $__tool_directory__
        --input_medium $input_medium
        --input_ras $input_ras
        --output_type "${",".join(map(str, $output_types))}"
        --out_log $log
        #if $cond_model.model_selector == 'Custom'
            --model $model
            --model_name $model.element_identifier
        #end if
        ]]>
    </command>

    <inputs>


        <param name="input_ras" argument="--input_ras" multiple="false" type="data" format="tabular, csv, tsv" label="RAS matrix:" />

        <param name="input_medium" argument="--input_medium" multiple="false" type="data" format="tabular, csv, tsv" label="Medium:"/>

        <param type="select" argument="--output_types" multiple="true" name="output_types" label="Desired outputs">
            <option value="FBA" selected="false">FBA</option>
            <option value="pFBA" selected="false">pFBA</option>
            <option value="FVA" selected="false">FVA</option>
            <option value="sensitivity" selected="false">Sensitivity knock-out</option>
        </param>
        
    </inputs>

        		
    <outputs>
        <data format="txt" name="log" label="modelGenerator - Log" />
        <collection name="results" type="list" label="${tool.name} - Results">
            <discover_datasets pattern="__name_and_ext__" directory="model_generator"/>
        </collection>
    </outputs>
       
        
    <help>
    <![CDATA[
What it does
-------------

This tool generates flux 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. It can be a single model, multiple models or a collection of models. 

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

The tool generates:
    - Samples: reporting the sampled fluxes for each reaction. Format: csv or pickle.
    - a log file (.txt).

**TIP**: The Batches parameter is useful to mantain in memory just a batch of samples at time. For example, if you wish to sample 10.000 points, than it is suggested to select n_samples = 1.000 and n_batches=10.


]]>
    </help>
    <expand macro="citations" />
</tool>