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comparison flux_sampling.xml @ 104:bf759eb48bf2 draft

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author luca_milaz
date Thu, 27 Jun 2024 12:07:50 +0000
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103:7956fd703ea3 104:bf759eb48bf2
1 <tool id="fluxSampling" name="COBRAxy Model sampling" version="2.0.0">
2
3 <macros>
4 <import>marea_macros.xml</import>
5 </macros>
6
7 <requirements>
8 <requirement type="package" version="0.29.0">cobra</requirement>
9 <requirement type="package" version="4.9.3">lxml</requirement>
10 </requirements>
11
12 <command detect_errors="exit_code">
13 <![CDATA[
14 python $__tool_directory__/flux_sampling.py
15 --input $input
16 --name $input.element_identifier
17 #if $algorithm_param.algorithm == 'OPTGP':
18 --thinning $thinning
19 --n_batches $n_batches
20 --n_samples $n_samples
21 --seed $seed
22 --output_format $output_format
23 --out_log $log
24 ]]>
25 </command>
26 <inputs>
27 <param name="input" argument="--input" type="data" format="xml, json" label="Model:" />
28
29 <conditional name="algorithm_param">
30 <param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:">
31 <option value="CBS" selected="true">CBS</option>
32 <option value="OPTGP">OPTGP</option>
33 </param>
34 <when value="OPTGP">
35 <param name="thinning" argument="--thinning" type="integer" label="Thinning:" />
36 </when>
37
38 </conditional>
39
40 <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" default="1"/>
41
42 <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" default="1000"/>
43
44 <param name="seed" argument="--seed" type="integer" label="Seed:" default="0"/>
45
46 <param name="output_format" argument="--output_format" type="select" label="Output files format:">
47 <option value="p" selected="true">pickle extension (binary, non-editable, pre-parsed)</option>
48 <option value="csv">Comma Separated Values (csv text file, editable, raw)</option>
49 </param>
50 </inputs>
51
52 <outputs>
53 <data format="txt" name="log" label="fluxSampling - $name - Log" />
54
55 <collection name="results" type="list" label="Model sampling result ($output_format)">
56 <discover_datasets name = "collection" pattern="__name_and_ext__" directory="result"/>
57 </collection>
58 </outputs>
59
60 <help>
61 <![CDATA[
62 What it does
63 -------------
64
65 This tool generates feasible 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.
66
67 Accepted files:
68 - A model: JSON or XML file reporting reactions and rules contained in the model.
69
70
71 Output:
72 -------------
73
74 The tool generates:
75 - Samples: reporting the sampled fluxes for each reaction in the custom model given. Format: csv or pickle.
76 - a log file (.txt).
77 ]]>
78 </help>
79 <expand macro="citations" />
80 </tool>