annotate Marea/ras_generator.xml @ 68:aa09186cbc9f draft

Uploaded
author bimib
date Thu, 23 Apr 2020 17:03:48 -0400
parents 88b7180d7b79
children 11335fd2dda0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
52
88b7180d7b79 Uploaded
bimib
parents: 51
diff changeset
1 <tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.6">
47
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
2 <description>- Reaction Activity Scores computation</description>
45
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
3 <macros>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
4 <import>marea_macros.xml</import>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
5 </macros>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
6 <requirements>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
7 <requirement type="package" version="0.23.0">pandas</requirement>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
8 <requirement type="package" version="1.1.0">scipy</requirement>
49
2c2a11aa1e02 fix dependencies
bimib
parents: 48
diff changeset
9 <requirement type="package" version="0.17.1">cobra</requirement>
45
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
10 <requirement type="package" version="4.2.1">lxml</requirement>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
11 <requirement type="package" version="0.8.1">svglib</requirement>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
12 <requirement type="package" version="3.4.0">reportlab</requirement>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
13 </requirements>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
14 <command detect_errors="exit_code">
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
15 <![CDATA[
47
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
16 python $__tool_directory__/ras_generator.py
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
17 --rules_selector $cond_rule.rules_selector
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
18 --input $input
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
19 --none $none
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
20 --tool_dir $__tool_directory__
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
21 --out_log $log
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
22 --ras_output $ras_output
52
88b7180d7b79 Uploaded
bimib
parents: 51
diff changeset
23 #if $cond_rule.rules_selector == 'Custom'
88b7180d7b79 Uploaded
bimib
parents: 51
diff changeset
24 --custom $cond_rule.Custom_rules
88b7180d7b79 Uploaded
bimib
parents: 51
diff changeset
25 #end if
45
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
26 ]]>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
27 </command>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
28 <inputs>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
29 <conditional name="cond_rule">
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
30 <expand macro="options"/>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
31 <when value="HMRcore">
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
32 </when>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
33 <when value="Recon">
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
34 </when>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
35 <when value="Custom">
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
36 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
37 </when>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
38 </conditional>
47
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
39 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
40 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
41 <param name="none" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
45
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
42 </inputs>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
43
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
44 <outputs>
47
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
45 <data format="txt" name="log" label="Expression2RAS - $name - Log" />
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
46 <data format="tabular" name="ras_output" label="$name RAS"/>
45
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
47 </outputs>
47
3af9d394367c Uploaded
bimib
parents: 45
diff changeset
48
45
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
49 <help>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
50 <![CDATA[
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
51
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
52 What it does
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
53 -------------
48
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
54
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
55 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.
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
56
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
57 Accepted files:
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
58 - A gene expression dataset
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
59
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
60 Format:
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
61 Tab-separated text file reporting the normalized expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column).
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
62 Column header: sample ID.
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
63 Row header: gene ID.
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
64
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
65
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
66 Optional files:
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
67 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
68
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
69 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
70 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
71
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
72 Computation option ‘(A and NaN) solved as (A)’:
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
73 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’
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
74
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
75 If YES is selected: the GPR will be solved as A.
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
76
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
77 If NO is selected: the GPR will be disregarded tout-court (i.e., treated as NaN).
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
78
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
79 Example input
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
80 -------------
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
81
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
82 Custom GPR rules:
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
83
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
84 +------------+--------------------------------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
85 | id | rule (with entrez-id |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
86 +============+======================================+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
87 | r1642 | 155060 or 10357 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
88 +------------+--------------------------------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
89 | r1643 | 155060 or 100134869 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
90 +------------+--------------------------------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
91 | r1640 | 155060 and 100134869 or 10357 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
92 +------------+--------------------------------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
93
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
94 RNA-seq dataset:
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
95
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
96 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
97 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
98 +============+================+================+================+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
99 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
100 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
101 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
102 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
103 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
104 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
105 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
106 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
107 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
108 +------------+----------------+----------------+----------------+
e4235b5231e4 Uploaded
bimib
parents: 47
diff changeset
109
45
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
110 ]]>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
111 </help>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
112 <expand macro="citations" />
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
113 </tool>
7aa966c488a4 Uploaded
bimib
parents:
diff changeset
114