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comparison COBRAxy/flux_simulation.xml @ 4:41f35c2f0c7b draft

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author luca_milaz
date Wed, 18 Sep 2024 10:59:10 +0000
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3:1f3ac6fd9867 4:41f35c2f0c7b
1 <tool id="fluxSimulation" name="Flux Simulation" version="2.0.0">
2
3 <macros>
4 <import>marea_macros.xml</import>
5 </macros>
6
7 <requirements>
8 <requirement type="package" version="1.24.4">numpy</requirement>
9 <requirement type="package" version="2.0.3">pandas</requirement>
10 <requirement type="package" version="0.29.0">cobra</requirement>
11 <requirement type="package" version="5.2.2">lxml</requirement>
12 <requirement type="package" version="1.4.2">joblib</requirement>
13 <requirement type="package" version="1.10.1">scipy</requirement>
14 </requirements>
15
16 <command detect_errors="exit_code">
17 <![CDATA[
18 python $__tool_directory__/flux_simulation.py
19 --tool_dir $__tool_directory__
20 --model_selector $cond_model.model_selector
21 #if $cond_model.model_selector == 'Custom'
22 --model $model
23 --model_name $model.element_identifier
24 #end if
25 --input "${",".join(map(str, $inputs))}"
26 #set $names = ""
27 #for $input_temp in $inputs:
28 #set $names = $names + $input_temp.element_identifier + ","
29 #end for
30 --name $names
31 --thinning 0
32 #if $algorithm_param.algorithm == 'OPTGP':
33 --thinning $algorithm_param.thinning
34 #end if
35 --algorithm $algorithm_param.algorithm
36 --n_batches $n_batches
37 --n_samples $n_samples
38 --seed $seed
39 --output_type "${",".join(map(str, $output_types))}"
40 --output_type_analysis "${",".join(map(str, $output_types_analysis))}"
41 --out_log $log
42 ]]>
43 </command>
44 <inputs>
45
46 <conditional name="cond_model">
47 <expand macro="options_ras_to_bounds_model"/>
48 <when value="Custom">
49 <param name="model" argument="--model" type="data" format="json, xml" label="Custom model" />
50 </when>
51 </conditional>
52
53 <param name="inputs" argument="--inputs" multiple="true" type="data" format="tabular, csv, tsv" label="Bound(s):" />
54
55
56 <conditional name="algorithm_param">
57 <param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:">
58 <option value="CBS" selected="true">CBS</option>
59 <option value="OPTGP">OPTGP</option>
60 </param>
61 <when value="OPTGP">
62 <param name="thinning" argument="--thinning" type="integer" label="Thinning:" value="100" help="Number of iterations to wait before taking a sample."/>
63 </when>
64
65 </conditional>
66
67
68 <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" value="1000"/>
69
70 <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" value="10" help="This is useful for computational perfomances."/>
71
72 <param name="seed" argument="--seed" type="integer" label="Seed:" value="0" helph="Random seed."/>
73
74 <param type="select" argument="--output_types" multiple="true" name="output_types" label="Desired outputs from sampling">
75 <option value="mean" selected="true">Mean</option>
76 <option value="median" selected="true">Median</option>
77 <option value="quantiles" selected="true">Quantiles</option>
78 <option value="fluxes" selected="false">All fluxes</option>
79 </param>
80
81 <param type="select" argument="--output_types_analysis" multiple="true" name="output_types_analysis" label="Desired outputs from flux analysis">
82 <option value="pFBA" selected="false">pFBA</option>
83 <option value="FVA" selected="false">FVA</option>
84 <option value="sensitivity" selected="false">Sensitivity reaction knock-out (Biomass)</option>
85 </param>
86 </inputs>
87
88
89 <outputs>
90 <data format="txt" name="log" label="fluxSimulation - Log" />
91 <collection name="results" type="list" label="${tool.name} - Samples">
92 <discover_datasets pattern="__name_and_ext__" directory="flux_simulation"/>
93 </collection>
94 </outputs>
95
96
97 <help>
98 <![CDATA[
99 What it does
100 -------------
101
102 This tool generates flux samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) and OPTGP (mproved Artificial Centering Hit-and-Run sampler) sampling algorithms.
103 It can return sampled fluxes by appliying summary statistics:
104 - mean
105 - median
106 - quantiles (0.25, 0.50, 0.75).
107 Moreover, flux analysis can be perfomed over the metabolic model:
108 - parsimoniuos-FBA (optimized by Biomass)
109 - FVA
110 - Biomass sensitivity analysis (single reaction knock-out). It the ratio between the optimal FBA coefficients of the Biomass reaction after knocking-out a reaction and the same over the complete model.
111
112 Accepted files:
113 - A model: JSON or XML file reporting reactions and rules contained in the model. It can be a single model, multiple models or a collection of models.
114 - Cell-specific bounds: generated by RAS to Bounds tool.
115
116 Output:
117 -------------
118
119 The tool generates:
120 - Samples: reporting the sampled fluxes for each reaction. Format: csv.
121 - a log file (.txt).
122
123 **TIP**: The Batches parameter is useful to mantain in memory just a batch of samples at time. For example, if you wish to sample 10.000 points, than it is suggested to select n_samples = 1.000 and n_batches=10.
124
125
126 ]]>
127 </help>
128 <expand macro="citations" />
129 </tool>