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planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
author iuc
date Fri, 13 Dec 2024 21:32:42 +0000
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1 <tool id="gem_check_memote" name="Make GEM quality report" version="@VERSION@" profile="@PROFILE@">
2 <description>
3 using memote
4 </description>
5 <macros>
6 <import>gem_macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <expand macro="version_command_memote"/>
10 <command>
11 memote report snapshot
12 '${cb_model_location}'
13 --filename '${output}'
14 </command>
15 <inputs>
16 <expand macro="input_model"/>
17 </inputs>
18 <outputs>
19 <data name="output" format="html" label="${tool.name} on ${on_string}"/>
20 </outputs>
21 <tests>
22 <!-- Test 1: Valid E. coli core model -->
23 <test>
24 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
25 <output name="output">
26 <assert_contents>
27 <has_text text="Stoichiometric Consistency"/>
28 </assert_contents>
29 </output>
30 </test>
31 <!-- Test 2: Invalid model format -->
32 <test expect_failure="true">
33 <param name="cb_model_location" value="invalid_format.txt"/>
34 <assert_stderr>
35 <has_text text="Most likely the SBML model is not valid"/>
36 </assert_stderr>
37 </test>
38 </tests>
39 <help><![CDATA[
40 Memote Model Quality Check
41
42 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.
43
44 Inputs
45
46 `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.
47
48 Outputs
49
50 `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.
51
52 Usage Example
53
54 1. Upload your SBML model file.
55 2. Run the tool to generate the Memote report.
56 3. Review the report to identify any errors or areas for improvement in the model.
57
58 Troubleshooting
59
60 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.
61
62 References
63
64 Full documentation and further examples can be found at: https://doi.org/10.1038/s41587-020-0446-y
65 ]]></help>
66 <citations>
67 <expand macro="citation_memote"/>
68 </citations>
69 </tool>