--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gem_flux_distribution.xml	Fri Dec 13 21:33:11 2024 +0000
@@ -0,0 +1,81 @@
+<tool id="gem_flux_distribution" name="Calculate flux distribution" version="@VERSION@" profile="@PROFILE@">
+    <description> 
+        of a GEM
+    </description>
+    <macros>
+        <import>gem_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command_cobra"/>
+    <command>
+        python '$__tool_directory__/gem_flux_distribution.py'
+            --cb_model_location '${cb_model_location}'
+            -output '${output}'
+            --uptake_constraints_file '${uptake_constraints_file}'
+    </command>
+    <inputs>
+        <expand macro="input_model"/>
+        <expand macro="input_uptake_constraints"/>
+    </inputs>
+    <outputs>
+        <expand macro="output"/>
+    </outputs>
+    <tests>
+        <!-- Ensuring that minimal_gem.xml with minimal_gem_exchange_reactions.csv runs -->
+        <test>
+            <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
+            <param name="uptake_constraints_file" value="textbook_model_cobrapy_exchange.csv"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="reaction_name;reaction_id;flux"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test 2: Invalid model format -->
+        <test expect_failure="true">
+            <param name="cb_model_location" value="invalid_format.txt"/>
+            <assert_stderr>
+                <has_text text="The model could not be read"/>
+            </assert_stderr>
+        </test>
+        <expand macro="test_invalid_model"/>
+    </tests>
+    <help><![CDATA[
+        Flux distribution
+
+        This tool performs Flux Balance Analysis (FBA) to calculate the optimal flux distribution of a Genome-scale Metabolic Model (GEM).
+
+        What it does
+
+        * Reads a SBML-formatted metabolic model
+        * Applies user-specified uptake constraints
+        * Calculates the optimal flux distribution using FBA
+        * Outputs the results in CSV format
+
+        Input files
+
+        *Model file** (required): Must be in SBML format (.xml), compatible with COBRApy
+        *Uptake constraints file* (optional): CSV format
+
+        Output
+
+        The tool generates a CSV file containing:
+        * Reaction IDs
+        * Calculated flux values for each reaction
+        * Optimal flux distribution based on the model's objective function
+
+        Common Issues
+
+        If the tool fails, check:
+        * Is your SBML model valid?
+        * Are the uptake constraints properly formatted?
+        * Are the reaction IDs in the constraints file matching those in the model?
+        * Does your model have a valid objective function?
+
+        For more information about FBA, visit: http://cobrapy.readthedocs.io/
+    ]]></help>
+    <citations>
+        <expand macro="citation_pandas"/>
+        <expand macro="citation_cobrapy"/>
+    </citations>
+</tool>