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comparison Marea/ras_generator.xml @ 48:e4235b5231e4 draft

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author bimib
date Sun, 23 Feb 2020 09:41:14 -0500
parents 3af9d394367c
children 2c2a11aa1e02
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47:3af9d394367c 48:e4235b5231e4
1 <tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.2"> 1 <tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.3">
2 <description>- Reaction Activity Scores computation</description> 2 <description>- Reaction Activity Scores computation</description>
3 <macros> 3 <macros>
4 <import>marea_macros.xml</import> 4 <import>marea_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
29 </when> 29 </when>
30 <when value="Recon"> 30 <when value="Recon">
31 </when> 31 </when>
32 <when value="Custom"> 32 <when value="Custom">
33 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> 33 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
34 <conditional name="cond_map">
35 <param name="yes_no" type="select" label="Custom map? (optional)">
36 <option value="no" selected="true">no</option>
37 <option value="yes">yes</option>
38 </param>
39 <when value="yes">
40 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
41 </when>
42 <when value="no">
43 </when>
44 </conditional>
45 </when> 34 </when>
46 </conditional> 35 </conditional>
47 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" /> 36 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
48 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> 37 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
49 <param name="none" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 38 <param name="none" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
57 <help> 46 <help>
58 <![CDATA[ 47 <![CDATA[
59 48
60 What it does 49 What it does
61 ------------- 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
62 ]]> 107 ]]>
63 </help> 108 </help>
64 <expand macro="citations" /> 109 <expand macro="citations" />
65 </tool> 110 </tool>
66 111