Mercurial > repos > bimib > cobraxy

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author luca_milaz
date Wed, 18 Sep 2024 10:59:10 +0000
parents
children deb6d3439342
comparison
equal deleted inserted replaced
3:1f3ac6fd9867 4:41f35c2f0c7b
1 <tool id="CustomDataGenerator" name="Custom Data Generator" 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 </requirements>
13
14 <command detect_errors="exit_code">
15 <![CDATA[
16 python $__tool_directory__/custom_data_generator.py
17 --input $input
18 --name $input.element_identifier
19 --output_format $output_format
20 --out_log $log
21 ]]>
22 </command>
23 <inputs>
24 <param name="input" argument="--input" type="data" format="xml, json" label="Custom model:" />
25 <param name="name" argument="--name" type="text" label="Model's name:" value="Model" help="Default: Model" />
26
27 <param name="output_format" argument="--output_format" type="select" label="Output files format:">
28 <option value="p" selected="true">pickle extension (binary, non-editable, pre-parsed)</option>
29 <option value="csv">Comma Separated Values (csv text file, editable, raw)</option>
30 </param>
31 </inputs>
32
33 <outputs>
34 <data format="txt" name="log" label="CustomDataGenerator - $name - Log" />
35
36 <collection name="results" type="list" label="Custom Data Results ($output_format)">
37 <discover_datasets name = "collection" pattern="__name_and_ext__" directory="result"/>
38 </collection>
39 </outputs>
40
41 <help>
42 <![CDATA[
43 What it does
44 -------------
45
46 This tool generates two files containing reactions and rules respectively, starting from a custom model in JSON or XML format, that can be used as inputs for the RAS and RPS generator modules.
47
48 Accepted files:
49 - A model: JSON or XML file reporting reactions and rules contained in the model.
50
51
52 Output:
53 -------------
54
55 The tool generates:
56 - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle.
57 - reactions: reporting the reactions in the custom model given. Format: csv or pickle.
58 - a log file (.txt).
59 ]]>
60 </help>
61 <expand macro="citations" />
62 </tool>