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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 21:31:07 +0000
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8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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1 <tool id="gem_check_memote" name="Make GEM quality report" version="@VERSION@" profile="@PROFILE@">
8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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2 <description>
8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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3 using memote
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4 </description>
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5 <macros>
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6 <import>gem_macros.xml</import>
8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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7 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="version_command_memote"/>
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10 <command>
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11 memote report snapshot
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12 '${cb_model_location}'
8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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13 --filename '${output}'
8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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14 </command>
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15 <inputs>
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16 <expand macro="input_model"/>
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="html" label="${tool.name} on ${on_string}"/>
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20 </outputs>
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21 <tests>
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22 <!-- Test 1: Valid E. coli core model -->
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23 <test>
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24 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
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25 <output name="output">
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26 <assert_contents>
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27 <has_text text="Stoichiometric Consistency"/>
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28 </assert_contents>
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29 </output>
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30 </test>
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31 <!-- Test 2: Invalid model format -->
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32 <test expect_failure="true">
8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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33 <param name="cb_model_location" value="invalid_format.txt"/>
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34 <assert_stderr>
8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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35 <has_text text="Most likely the SBML model is not valid"/>
8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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36 </assert_stderr>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 Memote Model Quality Check
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41
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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.
8cc4ec2901e7 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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43
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44 Inputs
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45
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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.
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47
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48 Outputs
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49
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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.
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51
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52 Usage Example
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53
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54 1. Upload your SBML model file.
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55 2. Run the tool to generate the Memote report.
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56 3. Review the report to identify any errors or areas for improvement in the model.
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57
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58 Troubleshooting
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59
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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.
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61
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62 References
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63
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64 Full documentation and further examples can be found at: https://doi.org/10.1038/s41587-020-0446-y
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65 ]]></help>
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66 <citations>
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67 <expand macro="citation_memote"/>
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68 </citations>
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69 </tool>