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comparison Marea/ras_generator.xml @ 88:66432fdf1768 draft

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author bimib
date Mon, 07 Jun 2021 14:15:08 +0000
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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="0.25.3">pandas</requirement>
8 <requirement type="package" version="1.6.3">scipy</requirement>
9 <requirement type="package" version="4.6.3">lxml</requirement>
10 <requirement type="package" version="1.1.0">svglib</requirement>
11 <requirement type="package" version="3.5.67">reportlab</requirement>
12 </requirements>
13 <command detect_errors="exit_code">
14 <![CDATA[
15 python $__tool_directory__/ras_generator.py
16 --rules_selector $cond_rule.rules_selector
17 --input $input
18 --none $none
19 --tool_dir $__tool_directory__
20 --out_log $log
21 --ras_output $ras_output
22 #if $cond_rule.rules_selector == 'Custom'
23 --custom $cond_rule.Custom_rules
24 #end if
25 ]]>
26 </command>
27 <inputs>
28 <conditional name="cond_rule">
29 <expand macro="options"/>
30 <when value="HMRcore">
31 </when>
32 <when value="Recon">
33 </when>
34 <when value="Custom">
35 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
36 </when>
37 </conditional>
38 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
39 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
40 <param name="none" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
41 </inputs>
42
43 <outputs>
44 <data format="txt" name="log" label="Expression2RAS - $name - Log" />
45 <data format="tabular" name="ras_output" label="$name RAS"/>
46 </outputs>
47
48 <help>
49 <![CDATA[
50
51 What it does
52 -------------
53
54 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.
55
56 Accepted files:
57 - A gene expression dataset
58
59 Format:
60 Tab-separated text file reporting the normalized expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column).
61 Column header: sample ID.
62 Row header: gene ID.
63
64
65 Optional files:
66 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
67
68 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
69 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
70
71 Computation option ‘(A and NaN) solved as (A)’:
72 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’
73
74 If YES is selected: the GPR will be solved as A.
75
76 If NO is selected: the GPR will be disregarded tout-court (i.e., treated as NaN).
77
78 Example input
79 -------------
80
81 Custom GPR rules:
82
83 +------------+--------------------------------------+
84 | id | rule (with entrez-id |
85 +============+======================================+
86 | r1642 | 155060 or 10357 |
87 +------------+--------------------------------------+
88 | r1643 | 155060 or 100134869 |
89 +------------+--------------------------------------+
90 | r1640 | 155060 and 100134869 or 10357 |
91 +------------+--------------------------------------+
92
93 RNA-seq dataset:
94
95 +------------+----------------+----------------+----------------+
96 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
97 +============+================+================+================+
98 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
99 +------------+----------------+----------------+----------------+
100 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
101 +------------+----------------+----------------+----------------+
102 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
103 +------------+----------------+----------------+----------------+
104 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
105 +------------+----------------+----------------+----------------+
106 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
107 +------------+----------------+----------------+----------------+
108
109 ]]>
110 </help>
111 <expand macro="citations" />
112 </tool>
113