<tool id="MaREA RPS Generator" name="Expression2RPS" version="2.0.0">
    <description>- Reaction Propensity Scores computation</description>
    <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="5.2.2">lxml</requirement>
		<requirement type="package" version="0.29.0">cobra</requirement>
	</requirements>
    <command detect_errors="exit_code">
        <![CDATA[
      	python $__tool_directory__/rps_generator.py
        --input $input
      	--reaction_choice $cond_reactions.reaction_choice	
        --tool_dir $__tool_directory__
        --out_log $log	
        --rps_output $rps_output
        #if $cond_reactions.reaction_choice == 'custom'
        	--custom $cond_reactions.Custom_react
        #end if
        ]]>
    </command>
    <inputs>
        <param name="input" argument="--input" type="data" format="tabular, tsv, csv" label="Abundance dataset:" />
        <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset_RPS" help="Default: Dataset_RPS. Do not use white spaces." />
        
        <conditional name="cond_reactions">
			<param name="reaction_choice" argument="--reaction_choice" type="select" label="Choose reaction dataset:">
                	<option value="default" selected="true">ENGRO2 reaction dataset </option>
                	<option value="custom">Custom reaction dataset</option>
        	</param>
            <when value="custom">
                <param name="Custom_react" type="data" format="csv" label="Custom reactions" />
            </when>
        </conditional>  
    </inputs>

    <outputs>
        <data format="txt" name="log" label="Expression2RPS - $name - Log" />
        <data format="tabular" name="rps_output" label="$name"/>
    </outputs>

    <help>
<![CDATA[

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

This tool computes Reaction Propensity Scores based on the availability of reaction substrates, for (ideally) each input model reaction and for each sample. 
The score is computed as the product of the concentrations of the reacting substances, with each concentration raised to a power equal to its stoichiometric coefficient. According to themass action law, the rate of any chemical reaction is indeed proportional to this product.
This assumption holds as long as the substrate is in significant excess over the enzyme constant KM.
If a metabolite is either missing in the model provided with respect to its reactions or it is present in our "black list", the RPS score is set to NaN.
This "black list" of metabolites contains those substrates that are present in too many reactions to be significant. It is defined in the file black_list.pickle and cannot be modified by the user. 
 
Accepted files:
    - An abundance dataset: Tab-separated text file reporting the abundance value of each metabolite for each cell line in the dataset. 
                            Column header: cell line ID. 
                            Row header: metabolite ID.    

 
Optional files:
    - Custom reaction dataset: .csv file specifying for each reaction ID the corresponding formula.
                                First column: reaction ID
                                Second column: reaction formula.


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

The tool generates:
    - a tab-separated file(.csv): reporting the RPS values for each reaction and each cell line in the dataset.
    - a log file (.txt).
]]>
    </help>
<expand macro="citations" />
</tool>