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comparison ras_generator.xml @ 283:813439d60f85 draft

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author luca_milaz
date Mon, 08 Jul 2024 22:18:11 +0000
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282:d385c4df70c3 283:813439d60f85
1 <tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.7">
2 <description>- Reaction Activity Scores computation</description>
3 <macros>
4 <import>marea_macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="1.18.5">numpy</requirement>
8 <requirement type="package" version="1.4.4">pandas</requirement>
9 <requirement type="package" version="1.6.3">scipy</requirement>
10 <requirement type="package" version="4.6.3">lxml</requirement>
11 <requirement type="package" version="1.1.0">svglib</requirement>
12 <requirement type="package" version="3.5.67">reportlab</requirement>
13 </requirements>
14 <command detect_errors="exit_code">
15 <![CDATA[
16 python $__tool_directory__/ras_generator.py
17 --rules_selector $cond_rule.rules_selector
18 --input $input
19 --none $none
20 --tool_dir $__tool_directory__
21 --out_log $log
22 --ras_output $ras_output
23 #if $cond_rule.rules_selector == 'Custom'
24 --rule_list $rule_list
25 --rules_name $rule_list.element_identifier
26 #end if
27 ]]>
28 </command>
29 <inputs>
30 <conditional name="cond_rule">
31 <expand macro="options"/>
32 <when value="Custom">
33 <param name="rule_list" argument="--rule_list" type="data" format="tabular, csv, pickle, p, pk" label="Custom rules" />
34 </when>
35 </conditional>
36 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
37 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
38 <param name="none" argument="--none" type="boolean" checked="true" label="(A and NaN) solved as (A)?" />
39 </inputs>
40
41 <outputs>
42 <data format="txt" name="log" label="Expression2RAS - $name - Log" />
43 <data format="tabular" name="ras_output" label="$name RAS"/>
44 </outputs>
45
46 <help>
47 <![CDATA[
48
49 What it does
50 -------------
51
52 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.
53
54 Accepted files:
55 - A gene expression dataset
56
57 Format:
58 Tab-separated text file reporting the normalized expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column).
59 Column header: sample ID.
60 Row header: gene ID.
61
62
63 Optional files:
64 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
65
66 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
67 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
68
69 Computation option ‘(A and NaN) solved as (A)’:
70 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’
71
72 If YES is selected: the GPR will be solved as A.
73
74 If NO is selected: the GPR will be disregarded tout-court (i.e., treated as NaN).
75
76 Example input
77 -------------
78
79 Custom GPR rules:
80
81 +------------+--------------------------------------+
82 | id | rule (with entrez-id |
83 +============+======================================+
84 | r1642 | 155060 or 10357 |
85 +------------+--------------------------------------+
86 | r1643 | 155060 or 100134869 |
87 +------------+--------------------------------------+
88 | r1640 | 155060 and 100134869 or 10357 |
89 +------------+--------------------------------------+
90
91 RNA-seq dataset:
92
93 +------------+----------------+----------------+----------------+
94 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
95 +============+================+================+================+
96 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
97 +------------+----------------+----------------+----------------+
98 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
99 +------------+----------------+----------------+----------------+
100 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
101 +------------+----------------+----------------+----------------+
102 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
103 +------------+----------------+----------------+----------------+
104 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
105 +------------+----------------+----------------+----------------+
106
107 ]]>
108 </help>
109 <expand macro="citations" />
110 </tool>
111