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author iuc
date Fri, 13 Dec 2024 21:33:11 +0000
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1 <tool id="gem_flux_distribution" name="Calculate flux distribution" version="@VERSION@" profile="@PROFILE@">
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2 <description>
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3 of 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 '$__tool_directory__/gem_flux_distribution.py'
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12 --cb_model_location '${cb_model_location}'
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13 -output '${output}'
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14 --uptake_constraints_file '${uptake_constraints_file}'
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15 </command>
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16 <inputs>
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17 <expand macro="input_model"/>
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18 <expand macro="input_uptake_constraints"/>
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19 </inputs>
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20 <outputs>
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21 <expand macro="output"/>
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22 </outputs>
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23 <tests>
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24 <!-- Ensuring that minimal_gem.xml with minimal_gem_exchange_reactions.csv runs -->
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25 <test>
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26 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
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27 <param name="uptake_constraints_file" value="textbook_model_cobrapy_exchange.csv"/>
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28 <output name="output">
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29 <assert_contents>
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30 <has_line line="reaction_name;reaction_id;flux"/>
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31 </assert_contents>
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32 </output>
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33 </test>
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34 <!-- Test 2: Invalid model format -->
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35 <test expect_failure="true">
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36 <param name="cb_model_location" value="invalid_format.txt"/>
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37 <assert_stderr>
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38 <has_text text="The model could not be read"/>
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39 </assert_stderr>
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40 </test>
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41 <expand macro="test_invalid_model"/>
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42 </tests>
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43 <help><![CDATA[
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44 Flux distribution
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45
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46 This tool performs Flux Balance Analysis (FBA) to calculate the optimal flux distribution of a Genome-scale Metabolic Model (GEM).
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47
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48 What it does
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49
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50 * Reads a SBML-formatted metabolic model
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51 * Applies user-specified uptake constraints
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52 * Calculates the optimal flux distribution using FBA
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53 * Outputs the results in CSV format
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54
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55 Input files
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56
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57 *Model file** (required): Must be in SBML format (.xml), compatible with COBRApy
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58 *Uptake constraints file* (optional): CSV format
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59
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60 Output
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61
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62 The tool generates a CSV file containing:
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63 * Reaction IDs
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64 * Calculated flux values for each reaction
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65 * Optimal flux distribution based on the model's objective function
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66
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67 Common Issues
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68
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69 If the tool fails, check:
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70 * Is your SBML model valid?
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71 * Are the uptake constraints properly formatted?
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72 * Are the reaction IDs in the constraints file matching those in the model?
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73 * Does your model have a valid objective function?
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74
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75 For more information about FBA, visit: http://cobrapy.readthedocs.io/
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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>