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

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author luca_milaz
date Wed, 18 Sep 2024 10:59:10 +0000
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3:1f3ac6fd9867 4:41f35c2f0c7b
1 <tool id="MaREA RAS Generator" name="Expression2RAS" version="2.0.0">
2 <description>- Reaction Activity Scores computation</description>
3 <macros>
4 <import>marea_macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="1.24.4">numpy</requirement>
8 <requirement type="package" version="2.0.3">pandas</requirement>
9 <requirement type="package" version="5.2.2">lxml</requirement>
10 <requirement type="package" version="0.29.0">cobra</requirement>
11 </requirements>
12 <command detect_errors="exit_code">
13 <![CDATA[
14 python $__tool_directory__/ras_generator.py
15 --rules_selector $cond_rule.rules_selector
16 --input $input
17 --none $none
18 --tool_dir $__tool_directory__
19 --out_log $log
20 --ras_output $ras_output
21 #if $cond_rule.rules_selector == 'Custom'
22 --rule_list $rule_list
23 --rules_name $rule_list.element_identifier
24 #end if
25 ]]>
26 </command>
27 <inputs>
28 <conditional name="cond_rule">
29 <expand macro="options"/>
30 <when value="Custom">
31 <param name="rule_list" argument="--rule_list" type="data" format="tabular, csv, pickle, p, pk" label="Custom rules" />
32 </when>
33 </conditional>
34 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
35 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
36 <param name="none" argument="--none" type="boolean" checked="true" label="(A and NaN) solved as (A)?" />
37 </inputs>
38
39 <outputs>
40 <data format="txt" name="log" label="Expression2RAS - $name - Log" />
41 <data format="tabular" name="ras_output" label="$name RAS"/>
42 </outputs>
43
44 <help>
45 <![CDATA[
46
47 What it does
48 -------------
49
50 This tool computes Reaction Activity Scores from gene expression (RNA-seq) dataset(s), as described in Graudenzi et al. Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. Journal of Biomedical Informatics, 2018, 87: 37-49.
51
52 Accepted files:
53 - A gene expression dataset
54
55 Format:
56 Tab-separated text file reporting the normalized expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column).
57 Column header: sample ID.
58 Row header: gene ID.
59
60
61 Optional files:
62 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
63
64 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
65 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
66
67 Computation option ‘(A and NaN) solved as (A)’:
68 In case of missing expression value, referred to as NaN (Not a Number), for a gene joined with an AND operator in a given GPR rule, the rule ‘A and NaN’
69
70 If YES is selected: the GPR will be solved as A.
71
72 If NO is selected: the GPR will be disregarded tout-court (i.e., treated as NaN).
73
74 Example input
75 -------------
76
77 Custom GPR rules:
78
79 +------------+--------------------------------------+
80 | id | rule (with entrez-id |
81 +============+======================================+
82 | r1642 | 155060 or 10357 |
83 +------------+--------------------------------------+
84 | r1643 | 155060 or 100134869 |
85 +------------+--------------------------------------+
86 | r1640 | 155060 and 100134869 or 10357 |
87 +------------+--------------------------------------+
88
89 RNA-seq dataset:
90
91 +------------+----------------+----------------+----------------+
92 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
93 +============+================+================+================+
94 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
95 +------------+----------------+----------------+----------------+
96 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
97 +------------+----------------+----------------+----------------+
98 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
99 +------------+----------------+----------------+----------------+
100 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
101 +------------+----------------+----------------+----------------+
102 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
103 +------------+----------------+----------------+----------------+
104
105 ]]>
106 </help>
107 <expand macro="citations" />
108 </tool>
109