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comparison COBRAxy/flux_simulation.xml @ 93:7e703e546998 draft

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author luca_milaz
date Sun, 13 Oct 2024 11:41:34 +0000
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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="Flux Simulation - Log" />
91
92 <data name="output" format="tabular" label="Flux Simulation - Output">
93 <discover_datasets pattern="__name_and_ext__"
94 directory="flux_simulation" visible="true" />
95 </data>
96
97 </outputs>
98
99 <help>
100 <![CDATA[
101 What it does
102 -------------
103
104 This tool generates flux samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) or OPTGP (Improved Artificial Centering Hit-and-Run sampler) sampling algorithms.
105
106 It can return sampled fluxes by appliying summary statistics:
107 - mean
108 - median
109 - quantiles (0.25, 0.50, 0.75).
110
111 Flux analysis can be perfomed over the metabolic model:
112 - parsimoniuos-FBA (optimized by Biomass)
113 - FVA
114 - Biomass sensitivity analysis (single reaction knock-out). It is the ratio between the optimal of the Biomass reaction computed by FBA after knocking-out a reaction and the same over the complete model.
115
116 Accepted files:
117 - A model: JSON or XML file reporting reactions and rules contained in the model. It can be ENGRO2 or a custom model.
118 - Context-specific bounds: generated by RAS to Bounds tool. This can be a collection of bounds too (one bounds file per context).
119
120 Output:
121 -------------
122
123 The tool generates:
124 - Samples: reporting the sampled fluxes for each reaction (reaction names on the rows and sample names on the columns). Format: tab-separated.
125 - a log file (.txt).
126
127 **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.
128 **TIP**: The Thinning parameter of the OPTGP algorithm is useful to converge to a stationary distribution (see cited articles by Galuzzi, Milazzo and Damiani).
129
130 ]]>
131 </help>
132 <expand macro="citations_fluxes" />
133
134 </tool>