diff gem_flux_variability_analysis.xml @ 0:dfeabe31d865 draft default tip

planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gem_flux_variability_analysis.xml	Fri Dec 13 21:34:04 2024 +0000
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+<tool id="gem_flux_variability_analysis" name="Flux variability analysis (FVA)" version="@VERSION@" profile="@PROFILE@">
+    <description>
+        on a GEM
+    </description>
+    <macros>
+        <import>gem_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command_cobra"/>
+    <command>
+        python '$__tool_directory__/gem_flux_variability_analysis.py'
+            --cb_model_location '${cb_model_location}'
+            --output '${output}'
+            --fraction '${fraction_of_optimum}'
+            --uptake_constraints_file '${uptake_constraints_file}'
+    </command>
+    <inputs>
+        <expand macro="input_model"/>
+        <param name="fraction_of_optimum" min="0" max="1" type="float" value="0.99" label="Fraction of optimum required in FVA solutions"/>
+        <expand macro="input_uptake_constraints"/>
+    </inputs>
+    <outputs>
+        <expand macro="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
+            <param name="fraction_of_optimum" value="0.99"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="reaction_id;reaction_name;minimum;maximum"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
+            <param name="fraction_of_optimum" value="0.99"/>
+            <param name="uptake_constraints_file" value="textbook_model_cobrapy_exchange.csv"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line="reaction_id;reaction_name;minimum;maximum"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Flux Variability Analysis (FVA)
+
+        This tool performs Flux Variability Analysis (FVA) on a Genome-scale Metabolic Model (GEM). FVA is a method used to determine the minimum and maximum flux values that each reaction in the network can carry while maintaining a specific objective value.
+
+        Input Parameters
+
+        **Model File**: A GEM in SBML format (.xml) that will be analyzed.
+
+        **Fraction of Optimum**: A value between 0 and 1 that determines how much the objective function can deviate from its optimal value. For example:
+        - 1.0: Only solutions achieving 100% of optimal objective value
+        - 0.9: Solutions achieving at least 90% of optimal objective value
+        - 0.5: Solutions achieving at least 50% of optimal objective value
+
+        **Uptake Constraints File** (optional): A CSV file specifying constraints for exchange reactions. The file should contain columns for exchange reaction IDs and their corresponding bounds.
+
+        Output
+        
+        The tool generates a CSV file containing:
+        - Reaction IDs
+        - Minimum flux values
+        - Maximum flux values
+        for each reaction in the model.
+
+        Common Issues
+        
+        - Ensure your model is well-formatted and contains no structural errors
+        - Check that exchange reactions are properly defined
+        - Verify that the model is feasible under the given constraints
+        - Large models may require significant computation time
+    ]]></help>
+    <citations>
+        <expand macro="citation_pandas"/>
+        <expand macro="citation_cobrapy"/>
+    </citations>
+</tool>