Mercurial > repos > iuc > gem_flux_variability_analysis

comparison gem_flux_variability_analysis.xml @ 0:dfeabe31d865 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
author iuc
date Fri, 13 Dec 2024 21:34:04 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:dfeabe31d865
1 <tool id="gem_flux_variability_analysis" name="Flux variability analysis (FVA)" version="@VERSION@" profile="@PROFILE@">
2 <description>
3 on a GEM
4 </description>
5 <macros>
6 <import>gem_macros.xml</import>
7 </macros>
8 <expand macro="requirements"/>
9 <expand macro="version_command_cobra"/>
10 <command>
11 python '$__tool_directory__/gem_flux_variability_analysis.py'
12 --cb_model_location '${cb_model_location}'
13 --output '${output}'
14 --fraction '${fraction_of_optimum}'
15 --uptake_constraints_file '${uptake_constraints_file}'
16 </command>
17 <inputs>
18 <expand macro="input_model"/>
19 <param name="fraction_of_optimum" min="0" max="1" type="float" value="0.99" label="Fraction of optimum required in FVA solutions"/>
20 <expand macro="input_uptake_constraints"/>
21 </inputs>
22 <outputs>
23 <expand macro="output"/>
24 </outputs>
25 <tests>
26 <test>
27 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
28 <param name="fraction_of_optimum" value="0.99"/>
29 <output name="output">
30 <assert_contents>
31 <has_line line="reaction_id;reaction_name;minimum;maximum"/>
32 </assert_contents>
33 </output>
34 </test>
35 <test>
36 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
37 <param name="fraction_of_optimum" value="0.99"/>
38 <param name="uptake_constraints_file" value="textbook_model_cobrapy_exchange.csv"/>
39 <output name="output">
40 <assert_contents>
41 <has_line line="reaction_id;reaction_name;minimum;maximum"/>
42 </assert_contents>
43 </output>
44 </test>
45 </tests>
46 <help><![CDATA[
47 Flux Variability Analysis (FVA)
48
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.
50
51 Input Parameters
52
53 **Model File**: A GEM in SBML format (.xml) that will be analyzed.
54
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:
56 - 1.0: Only solutions achieving 100% of optimal objective value
57 - 0.9: Solutions achieving at least 90% of optimal objective value
58 - 0.5: Solutions achieving at least 50% of optimal objective value
59
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.
61
62 Output
63
64 The tool generates a CSV file containing:
65 - Reaction IDs
66 - Minimum flux values
67 - Maximum flux values
68 for each reaction in the model.
69
70 Common Issues
71
72 - Ensure your model is well-formatted and contains no structural errors
73 - Check that exchange reactions are properly defined
74 - Verify that the model is feasible under the given constraints
75 - Large models may require significant computation time
76 ]]></help>
77 <citations>
78 <expand macro="citation_pandas"/>
79 <expand macro="citation_cobrapy"/>
80 </citations>
81 </tool>