|
45
|
1 <tool id="MaREA RAS Generator" name="RAS Generator" version="1.0.0">
|
|
|
2 <description></description>
|
|
|
3 <macros>
|
|
|
4 <import>marea_macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <requirements>
|
|
|
7 <requirement type="package" version="0.23.0">pandas</requirement>
|
|
|
8 <requirement type="package" version="1.1.0">scipy</requirement>
|
|
|
9 <requirement type="package" version="0.10.1">cobra</requirement>
|
|
|
10 <requirement type="package" version="4.2.1">lxml</requirement>
|
|
|
11 <requirement type="package" version="0.8.1">svglib</requirement>
|
|
|
12 <requirement type="package" version="3.4.0">reportlab</requirement>
|
|
|
13 </requirements>
|
|
|
14 <command detect_errors="exit_code">
|
|
|
15 <![CDATA[
|
|
|
16 python $__tool_directory__/marea.py
|
|
|
17 --rules_selector $cond_rule.rules_selector
|
|
|
18 --tool_dir $__tool_directory__
|
|
|
19 --option $cond.type_selector
|
|
|
20 --out_log $log
|
|
|
21 --input_datas ${input_Datasets}
|
|
|
22 --single_ras_file $ras_single
|
|
|
23 --none ${cond.None}
|
|
|
24 #end if
|
|
|
25 ]]>
|
|
|
26 </command>
|
|
|
27
|
|
|
28 <inputs>
|
|
|
29 <conditional name="cond_rule">
|
|
|
30 <expand macro="options"/>
|
|
|
31 <when value="HMRcore">
|
|
|
32 </when>
|
|
|
33 <when value="Recon">
|
|
|
34 </when>
|
|
|
35 <when value="Custom">
|
|
|
36 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
|
|
|
37 <conditional name="cond_map">
|
|
|
38 <param name="yes_no" type="select" label="Custom map? (optional)">
|
|
|
39 <option value="no" selected="true">no</option>
|
|
|
40 <option value="yes">yes</option>
|
|
|
41 </param>
|
|
|
42 <when value="yes">
|
|
|
43 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
|
|
|
44 </when>
|
|
|
45 <when value="no">
|
|
|
46 </when>
|
|
|
47 </conditional>
|
|
|
48 </when>
|
|
|
49 </conditional>
|
|
|
50 <conditional name="cond">
|
|
|
51
|
|
|
52 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
|
|
|
53 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
|
|
|
54 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
|
|
|
55
|
|
|
56
|
|
|
57 </when>
|
|
|
58 </conditional>
|
|
|
59 </inputs>
|
|
|
60
|
|
|
61 <outputs>
|
|
|
62 <data format="txt" name="log" label="MaREA - Log" />
|
|
|
63 <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
|
|
|
64 <filter>cond['type_selector'] == "datasets_rasonly"</filter>
|
|
|
65 </data>
|
|
|
66 <collection name="results" type="list" label="MaREA - Results">
|
|
|
67 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
|
|
|
68 <discover_datasets pattern="__name_and_ext__" directory="result"/>
|
|
|
69 </collection>
|
|
|
70 <collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
|
|
|
71 <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
|
|
|
72 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
|
|
|
73 </collection>
|
|
|
74
|
|
|
75 </outputs>
|
|
|
76 <tests>
|
|
|
77 <test>
|
|
|
78 <param name="pValue" value="0.56"/>
|
|
|
79 <output name="log" file="log.txt"/>
|
|
|
80 </test>
|
|
|
81 </tests>
|
|
|
82 <help>
|
|
|
83 <![CDATA[
|
|
|
84
|
|
|
85 What it does
|
|
|
86 -------------
|
|
|
87
|
|
|
88 This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724.
|
|
|
89
|
|
|
90 Accepted files are:
|
|
|
91 - option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*");
|
|
|
92 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
|
|
|
93
|
|
|
94 Optional files:
|
|
|
95 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
|
|
|
96
|
|
|
97 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
|
|
|
98 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
|
|
|
99 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
|
|
|
100
|
|
|
101 The tool generates:
|
|
|
102 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
|
|
|
103 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
|
|
|
104 3) a log file (.txt).
|
|
|
105
|
|
|
106 RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID.
|
|
|
107
|
|
|
108 Class-file format: each row of the class-file reports the sample ID (column1) and the label of the class/condition the sample belongs to (column 2).
|
|
|
109
|
|
|
110 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
|
|
|
111
|
|
|
112 Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA".
|
|
|
113
|
|
|
114
|
|
|
115 Example input
|
|
|
116 -------------
|
|
|
117
|
|
|
118 **"Custom Rules"** option:
|
|
|
119
|
|
|
120 Custom Rules Dastaset:
|
|
|
121
|
|
|
122 @CUSTOM_RULES_EXEMPLE@
|
|
|
123
|
|
|
124 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
|
|
|
125
|
|
|
126 RNA-seq Dataset 1:
|
|
|
127
|
|
|
128 @DATASET_EXEMPLE1@
|
|
|
129
|
|
|
130 RNA-seq Dataset 2:
|
|
|
131
|
|
|
132 @DATASET_EXEMPLE2@
|
|
|
133
|
|
|
134 **"RNAseq of all samples + sample group specification"** option:
|
|
|
135
|
|
|
136 RNA-seq Dataset:
|
|
|
137
|
|
|
138 @DATASET_EXEMPLE1@
|
|
|
139
|
|
|
140 Class-file:
|
|
|
141
|
|
|
142 +------------+------------+
|
|
|
143 | Patient_ID | class |
|
|
|
144 +============+============+
|
|
|
145 | TCGAAA3529 | MSI |
|
|
|
146 +------------+------------+
|
|
|
147 | TCGAA62671 | MSS |
|
|
|
148 +------------+------------+
|
|
|
149 | TCGAA62672 | MSI |
|
|
|
150 +------------+------------+
|
|
|
151
|
|
|
152 |
|
|
|
153
|
|
|
154 .. class:: infomark
|
|
|
155
|
|
|
156 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
|
|
|
157
|
|
|
158 .. class:: infomark
|
|
|
159
|
|
|
160 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
|
|
|
161
|
|
|
162 @REFERENCE@
|
|
|
163
|
|
|
164 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
|
|
|
165 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
|
|
|
166 .. _MaREA cluster analysis: http://link del tool di cluster.org
|
|
|
167
|
|
|
168 ]]>
|
|
|
169 </help>
|
|
|
170 <expand macro="citations" />
|
|
|
171 </tool>
|
|
|
172
|
