|
4
|
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
|
|
15
|
78 This tool generates the reactions bounds for a given metabolic model (JSON or XML format) both with and without the use of the Reaction Activity Scores (RAS) matrix generated by RAS generator.
|
|
|
79 Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For a custom medium, It is suggested to use the template file returned by the Custom Data Generator tool.
|
|
|
80 If the RAS matrix, generated by the RAS generator tool, is used, then a bounds file is generated for each cell. Otherwise, a single bounds file is returned.
|
|
4
|
81
|
|
|
82 Accepted files:
|
|
|
83 - A model: JSON or XML file reporting reactions and rules contained in the model.
|
|
|
84 - RAS matrix: tab-separated RAS file as returned by RAS generator.
|
|
|
85 - Medium: tab-separated file containing lower and upper-bounds of medium reactions.
|
|
|
86
|
|
15
|
87 Example of custum growth medium file:
|
|
4
|
88
|
|
17
|
89
|
|
4
|
90 +------------+----------------+----------------+
|
|
18
|
91 | Reaction ID| lower_bound | upper_bound |
|
|
4
|
92 +============+================+================+
|
|
|
93 | r1 | 0.123167 | 0.371355 |
|
|
|
94 +------------+----------------+----------------+
|
|
|
95 | r2 | 0.268765 | 0.765567 |
|
|
|
96 +------------+----------------+----------------+
|
|
|
97
|
|
|
98
|
|
|
99 Output:
|
|
|
100 -------------
|
|
|
101
|
|
|
102 The tool generates:
|
|
|
103 - bounds: reporting the bounds of the model, or cells if RAS is used. Format: tab-separated.
|
|
|
104 - a log file (.txt).
|
|
|
105 ]]>
|
|
|
106 </help>
|
|
|
107 <expand macro="citations" />
|
|
|
108 </tool> |
