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+++ b/COBRAxy/rps_generator.xml	Sun Oct 13 11:41:34 2024 +0000
@@ -0,0 +1,79 @@
+<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" help="Default: Dataset" />
+        
+        <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 RPS"/>
+    </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>
+