--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gem_check_memote.xml	Fri Dec 13 21:32:42 2024 +0000
@@ -0,0 +1,69 @@
+<tool id="gem_check_memote" name="Make GEM quality report" version="@VERSION@" profile="@PROFILE@">
+    <description>
+        using memote
+    </description>
+    <macros>
+        <import>gem_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command_memote"/>
+    <command>
+        memote report snapshot
+            '${cb_model_location}'
+            --filename '${output}'
+    </command>
+    <inputs>
+        <expand macro="input_model"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="html" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <!-- Test 1: Valid E. coli core model -->
+        <test>
+            <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="Stoichiometric Consistency"/>
+                </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="Most likely the SBML model is not valid"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Memote Model Quality Check
+
+        The GEM Check Memote tool runs the Memote test suite to generate a detailed report on the quality of a genome-scale metabolic model (GEM). Memote assesses various model characteristics such as stoichiometric consistency and model annotations.
+
+        Inputs
+
+        `Model to check with memote`: The metabolic model in SBML format (.xml or .sbml) to be analyzed by Memote. Ensure the file conforms to SBML standards.
+
+        Outputs
+
+        `Memote report`: An HTML file that contains the full results of the Memote assessment. This report includes overall model quality scores and highlights any issues that need correction.
+
+        Usage Example
+
+        1. Upload your SBML model file.
+        2. Run the tool to generate the Memote report.
+        3. Review the report to identify any errors or areas for improvement in the model.
+
+        Troubleshooting
+        
+        If the tool fails to run, ensure that your input file is a valid SBML model. Incorrect file formats or non-compliant models may trigger errors.
+
+        References
+        
+        Full documentation and further examples can be found at: https://doi.org/10.1038/s41587-020-0446-y
+    ]]></help>
+    <citations>
+        <expand macro="citation_memote"/>
+    </citations>
+</tool>