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comparison marea_2/ras_to_bounds.xml @ 179:11645e643642 draft

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author francesco_lapi
date Fri, 26 Jul 2024 15:27:36 +0000
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children 3f1cfd63fb81
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178:34239ccd2e41 179:11645e643642
1 <tool id="MaREA RAS to bounds" name="RAStoBounds" 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 </requirements>
14
15 <command detect_errors="exit_code">
16 <![CDATA[
17 python $__tool_directory__/ras_to_bounds.py
18 --tool_dir $__tool_directory__
19 --model_selector $cond_model.model_selector
20 #if $cond_model.model_selector == 'Custom'
21 --model $model
22 --model_name $model.element_identifier
23 #end if
24 --medium_selector $cond_medium.medium_selector
25 #if $cond_medium.medium_selector == 'Custom'
26 --medium $medium
27 #end if
28 --ras_selector $cond_ras.ras_choice
29 #if $cond_ras.ras_choice == "True"
30 --input_ras $cond_ras.input_ras
31 #end if
32 --out_log $log
33 ]]>
34 </command>
35 <inputs>
36 <conditional name="cond_model">
37 <expand macro="options_ras_to_bounds_model"/>
38 <when value="Custom">
39 <param name="model" argument="--model" type="data" format="json, xml" label="Custom model" />
40 </when>
41 </conditional>
42
43 <conditional name="cond_ras">
44 <param name="ras_choice" argument="--ras_choice" type="select" label="Do want to use RAS?">
45 <option value="True" selected="true">Yes</option>
46 <option value="False">No</option>
47 </param>
48 <when value="True">
49 <param name="input_ras" argument="--input_ras" multiple="false" type="data" format="tabular, csv, tsv" label="RAS matrix:" />
50 </when>
51 </conditional>
52
53 <conditional name="cond_medium">
54 <expand macro="options_ras_to_bounds_medium"/>
55 <when value="Custom">
56 <param name="medium" argument="--medium" type="data" format="tabular, csv, tsv" label="Custom medium" />
57 </when>
58 </conditional>
59
60 </inputs>
61
62 <outputs>
63 <data format="txt" name="log" label="RAStoBounds- Log" />
64
65 <collection name="ras_to_bounds" type="list" label="Ras to Bounds">
66 <discover_datasets name = "collection" pattern="__name_and_ext__" directory="ras_to_bounds"/>
67 </collection>
68
69 </outputs>
70
71 <help>
72
73 <![CDATA[
74
75 What it does
76 -------------
77
78 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.
79
80 Accepted files:
81 - A model: JSON or XML file reporting reactions and rules contained in the model.
82
83
84 Output:
85 -------------
86
87 The tool generates:
88 - rules: reporting the rules for each reaction in the custom model given. Format: csv or pickle.
89 - reactions: reporting the reactions in the custom model given. Format: csv or pickle.
90 - a log file (.txt).
91 ]]>
92 </help>
93 <expand macro="citations" />
94 </tool>