Mercurial > repos > iuc > gem_flux_variability_analysis

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author iuc
date Fri, 13 Dec 2024 21:32:00 +0000
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1 <tool id="gem_flux_variability_analysis" name="Flux variability analysis (FVA)" version="@VERSION@" profile="@PROFILE@">
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2 <description>
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3 on a GEM
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4 </description>
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5 <macros>
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6 <import>gem_macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="version_command_cobra"/>
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10 <command>
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11 python '$__tool_directory__/gem_flux_variability_analysis.py'
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12 --cb_model_location '${cb_model_location}'
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13 --output '${output}'
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14 --fraction '${fraction_of_optimum}'
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15 --uptake_constraints_file '${uptake_constraints_file}'
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16 </command>
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17 <inputs>
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18 <expand macro="input_model"/>
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19 <param name="fraction_of_optimum" min="0" max="1" type="float" value="0.99" label="Fraction of optimum required in FVA solutions"/>
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20 <expand macro="input_uptake_constraints"/>
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21 </inputs>
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22 <outputs>
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23 <expand macro="output"/>
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
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28 <param name="fraction_of_optimum" value="0.99"/>
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29 <output name="output">
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30 <assert_contents>
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31 <has_line line="reaction_id;reaction_name;minimum;maximum"/>
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32 </assert_contents>
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33 </output>
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34 </test>
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35 <test>
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36 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
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37 <param name="fraction_of_optimum" value="0.99"/>
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38 <param name="uptake_constraints_file" value="textbook_model_cobrapy_exchange.csv"/>
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39 <output name="output">
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40 <assert_contents>
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41 <has_line line="reaction_id;reaction_name;minimum;maximum"/>
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42 </assert_contents>
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43 </output>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 Flux Variability Analysis (FVA)
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48
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49 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.
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50
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51 Input Parameters
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52
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53 **Model File**: A GEM in SBML format (.xml) that will be analyzed.
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54
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55 **Fraction of Optimum**: A value between 0 and 1 that determines how much the objective function can deviate from its optimal value. For example:
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56 - 1.0: Only solutions achieving 100% of optimal objective value
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57 - 0.9: Solutions achieving at least 90% of optimal objective value
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58 - 0.5: Solutions achieving at least 50% of optimal objective value
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59
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60 **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.
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61
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62 Output
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63
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64 The tool generates a CSV file containing:
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65 - Reaction IDs
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66 - Minimum flux values
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67 - Maximum flux values
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68 for each reaction in the model.
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69
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70 Common Issues
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71
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72 - Ensure your model is well-formatted and contains no structural errors
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73 - Check that exchange reactions are properly defined
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74 - Verify that the model is feasible under the given constraints
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75 - Large models may require significant computation time
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76 ]]></help>
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77 <citations>
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78 <expand macro="citation_pandas"/>
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79 <expand macro="citation_cobrapy"/>
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80 </citations>
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81 </tool>