<tool id="MaREA RAS to bounds" name="RAStoBounds" version="2.0.0">
    
    <macros>
        <import>marea_macros.xml</import>
    </macros>

	<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>
        <requirement type="package" version="1.4.2">joblib</requirement>
	</requirements>

    <command detect_errors="exit_code">
        <![CDATA[
      	python $__tool_directory__/ras_to_bounds.py
        --tool_dir $__tool_directory__
        --model_selector $cond_model.model_selector
        #if $cond_model.model_selector == 'Custom'
            --model $model
            --model_name $model.element_identifier
        #end if
        --medium_selector $cond_medium.medium_selector
        #if $cond_medium.medium_selector == 'Custom'
            --medium $medium
        #end if
        --ras_selector $cond_ras.ras_choice
        #if $cond_ras.ras_choice == "True"
        	--input_ras $cond_ras.input_ras
        #end if
        --out_log $log
        ]]>
    </command>
    <inputs>
        <conditional name="cond_model">
            <expand macro="options_ras_to_bounds_model"/>
            <when value="Custom">
                <param name="model" argument="--model" type="data" format="json, xml" label="Custom model" />
            </when>
        </conditional> 

        <conditional name="cond_ras">
			<param name="ras_choice" argument="--ras_choice" type="select" label="Do want to use RAS?">
                	<option value="True" selected="true">Yes</option>
                	<option value="False">No</option>
        	</param>
            <when value="True">
                <param name="input_ras" argument="--input_ras" multiple="false" type="data" format="tabular, csv, tsv" label="RAS matrix:" />
            </when>
        </conditional>  
        
        <conditional name="cond_medium">
            <expand macro="options_ras_to_bounds_medium"/>
            <when value="Custom">
                <param name="medium" argument="--medium" type="data" format="tabular, csv, tsv" label="Custom medium" />
            </when>
        </conditional> 

    </inputs>

    <outputs>
        <data format="txt" name="log" label="RAStoBounds- Log" />
        
        <collection name="ras_to_bounds" type="list" label="Ras to Bounds">
            <discover_datasets name = "collection" pattern="__name_and_ext__" directory="ras_to_bounds"/>
        </collection>

    </outputs>

    <help>

    <![CDATA[

What it does
-------------

This tool generates the reactions bounds for a given metabolic model (JSON or XML format) both with and without the use of the Reaction Activity Scores (RAS) matrix generated by RAS generator.
Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For a custom medium, It is suggested to use the template file returned by the Custom Data Generator tool.
If the RAS matrix, generated by the RAS generator tool, is used, then a bounds file is generated for each cell. Otherwise, a single bounds file is returned.

Accepted files:
    - A model: JSON or XML file reporting reactions and rules contained in the model.   
    - RAS matrix: tab-separated RAS file as returned by RAS generator.
    - Medium: tab-separated file containing lower and upper-bounds of medium reactions.

Example of custum growth medium file:


+------------+----------------+----------------+
| Reaction ID|   lower_bound  |   upper_bound |  
+============+================+================+
| r1         |    0.123167    |    0.371355    | 
+------------+----------------+----------------+   
| r2         |    0.268765    |    0.765567    |  
+------------+----------------+----------------+   


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

The tool generates:
    - bounds: reporting the bounds of the model, or cells if RAS is used. Format: tab-separated.
    - a log file (.txt).
    ]]>
    </help>
    <expand macro="citations" />
</tool>