--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COBRAxy/ras_to_bounds.xml	Wed Sep 18 10:59:10 2024 +0000
@@ -0,0 +1,110 @@
+<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) with and without the injection of the Reaction Activity Scores (RAS) within the metabolic model.
+Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For 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 file of bounds 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 medium file
+-------------
+
+Custom medium:
+
++------------+----------------+----------------+
+| 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>
\ No newline at end of file