annotate COBRAxy/custom_data_generator.xml @ 392:f73d57641124 draft

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<tool id="CustomDataGenerator" name="Custom Data Generator" version="2.0.0">

	<requirements>
        <requirement type="package" version="1.24.4">numpy</requirement>
        <requirement type="package" version="2.0.3">pandas</requirement>
		<requirement type="package" version="0.29.0">cobra</requirement>
        <requirement type="package" version="5.2.2">lxml</requirement>
	</requirements>

    <macros>
        <import>marea_macros.xml</import>
    </macros>

    <command detect_errors="exit_code">
        <![CDATA[
      	python $__tool_directory__/custom_data_generator.py
        --tool_dir $__tool_directory__
        --medium_selector $cond_model.medium_selector
        #if $cond_model.model_selector == 'Custom_model'
            --input $cond_model.input
            --name $cond_model.name
        #else
            --model $cond_model.model_selector
            --name $cond_model.model_selector
        #end if
        #if $cond_model.medium_selector == 'Custom'
            --medium $cond_model.medium
        #end if

        --gene_format $gene_format
        
        --out_log $log
        --out_tabular $out_tabular
        ]]>
    </command>
    <inputs>
        <conditional name="cond_model">
            <expand macro="options_model"/>
            
            <!-- ENGRO2 -->
            <when value="ENGRO2">
                <param name="name" argument="--name" type="text" value="ENGRO2" hidden="true" />
                <conditional name="medium_selector">
                    <expand macro="options_ras_to_bounds_medium"/>
                    <when value="Custom">
                        <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
                    </when>
                </conditional>
            </when>

            <!-- Recon -->
            <when value="Recon">
                <param name="name" argument="--name" type="text" value="Recon" hidden="true" />
                <conditional name="medium_selector">
                    <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
                        <option value="Default" selected="true">Default (Recon built-in medium)</option>
                        <option value="Custom">Custom medium file</option>
                    </param>
                    <when value="Default">
                        <!-- Nessun parametro aggiuntivo necessario -->
                    </when>
                    <when value="Custom">
                        <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
                    </when>
                </conditional>
            </when>

            <!-- Custom model -->
            <when value="Custom_model">
                <param name="input" argument="--input" type="data" format="json,xml" label="Custom model file:" />
                <param name="name" argument="--name" type="text" label="Model's name:" value="CustomModel" />
                <conditional name="medium_selector">
                    <param name="medium_selector" argument="--medium_selector" type="select" label="Medium">
                        <option value="Default" selected="true">Don't use a separate medium file (use model defaults)</option>
                        <option value="Custom">Custom medium file (required)</option>
                    </param>
                    <when value="Default">
                        <!-- Nessun parametro aggiuntivo necessario -->
                    </when>
                    <when value="Custom">
                        <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" />
                    </when>
                </conditional>
            </when>
        </conditional>

        <param name="gene_format" argument="--gene_format" type="select" label="Gene nomenclature format:">
            <option value="Default" selected="true">Keep original gene nomenclature</option>
            <option value="ENSNG">ENSNG (Ensembl Gene ID)</option>
            <option value="HGNC_SYMBOL">HGNC Symbol</option>
            <option value="HGNC_ID">HGNC ID</option>
            <option value="ENTREZ">Entrez Gene ID</option>
        </param>
    </inputs>

    <outputs>
        <data name="log" format="txt" label="CustomDataGenerator - Log" />
        <data name="out_tabular" format="tabular" label="${cond_model.model_selector}_data_tabular" optional="true"/>
    </outputs>

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

This tool generates four files containing reactions, rules, reaction bounds and medium composition respectively, starting from a custom model in JSON or XML format.
Reactions and rules can be used as inputs for the RAS and RPS generator tools.

Accepted files:
    - A model: JSON, XML, MAT or YAML (.yml) file reporting reactions and rules contained in the model. Supported compressed formats: .zip, .gz and .bz2. Filename must follow the pattern: {model_name}.{extension}.[zip|gz|bz2]

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

The tool generates:
    - rules: reporting the rules for each reaction in the custom model given. Format: csv (tab separated).
    - reactions: reporting the reactions in the custom model given. Format: csv (tab separated).
    - reaction bounds: reporting the lower and upper bounds of each model reaction. Format: csv (tab separated).
    - medium composition: reporting the list of exchange/transport reactions. Format: csv (tab separated).
    - a log file (.txt).
    ]]>
    </help>
    <expand macro="citations" />
</tool>