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| <tool id="gem_check_memote" name="GEM check memote" version="0.17.0" profile="23.0"> | ||
| <description>Uses the Memote test suite to generate a quality report on a genome-scale metabolic model. See more at https://memote.readthedocs.io/en/latest/index.html</description> | ||
| <macros> | ||
| <import>gem_macros.xml</import> | ||
| </macros> | ||
| <requirements> | ||
| <requirement type="package" version="0.17.0">memote</requirement> | ||
| <requirement type="package" version="2.0.1">markupsafe</requirement> | ||
| </requirements> | ||
| <expand macro="version_command_memote"/> | ||
| <command> | ||
| python '$__tool_directory__/gem_check_memote.py' '--cb_model_location' '${cb_model_location}' '--output' '${output}' | ||
| </command> | ||
| <inputs> | ||
| <expand macro="input_model"/> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="html" label="Memote report"/> | ||
| </outputs> | ||
| <tests> | ||
| <!-- Test 1: Valid E. coli core model --> | ||
| <test> | ||
| <param name="cb_model_location" value="textbook_model_cobrapy.xml"/> | ||
| <output name="output"> | ||
| <assert_contents> | ||
| <has_text text="Stoichiometric Consistency"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <!-- Test 2: Invalid model format --> | ||
| <test expect_failure="true"> | ||
| <param name="cb_model_location" value="invalid_format.txt"/> | ||
| <assert_stderr> | ||
| <has_text text="Most likely the SBML model is not valid"/> | ||
| </assert_stderr> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| Memote Model Quality Check | ||
| <description>Uses the Memote test suite to generate a quality report on a genome-scale metabolic model. See more at https://memote.readthedocs.io/en/latest/index.html</description> | ||
| <macros> | ||
| <import>gem_macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <expand macro="version_command_memote"/> | ||
| <command> | ||
| memote report snapshot | ||
| '${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. | ||
| 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 | ||
| 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. | ||
| `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 | ||
| 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. | ||
| `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 | ||
| 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. | ||
| 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. | ||
| 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> | ||
| <citation type="bibtex"> | ||
| @article{lieven2020memote, | ||
| title={MEMOTE for standardized genome-scale metabolic model testing}, | ||
| author={Lieven, Christian and Beber, Moritz E and Olivier, Brett G and Bergmann, Frank T and Ataman, Meric and Babaei, Parizad and Bartell, Jennifer A and Blank, Lars M and Chauhan, Siddharth and Correia, Kevin and others}, | ||
| journal={Nature biotechnology}, | ||
| volume={38}, | ||
| number={3}, | ||
| pages={272--276}, | ||
| year={2020}, | ||
| publisher={Nature Publishing Group US New York} | ||
| } | ||
| </citation> | ||
| </citations> | ||
| 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> |
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