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comparison gem_flux_distribution.xml @ 0:1c71660496fb draft default tip

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