|
0
|
1 <tool id="MaREA" name="Metabolic Enrichment Analysis">
|
|
|
2 <description>for Galaxy</description>
|
|
1
|
3 <macros>
|
|
|
4 <import>marea_macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements" />
|
|
0
|
7 <requirements>
|
|
|
8 <requirement type="package">lxml</requirement>
|
|
|
9 <requirement type="package">svglib</requirement>
|
|
|
10 <requirement type="package">reportlab</requirement>
|
|
|
11 </requirements>
|
|
1
|
12 <command detect_errors="exit_code">
|
|
0
|
13 <![CDATA[
|
|
|
14 python $__tool_directory__/marea.py
|
|
|
15 --rules_selector $cond_rule.rules_selector
|
|
|
16 #if $cond_rule.rules_selector == 'Custom':
|
|
|
17 --custom ${cond_rule.Custom_rules}
|
|
|
18 --yes_no ${cond_rule.cond_map.yes_no}
|
|
|
19 #if $cond_rule.cond_map.yes_no == 'yes':
|
|
|
20 --custom_map $cond_rule.cond_map.Custom_map
|
|
|
21 #end if
|
|
|
22 #end if
|
|
|
23 --none $None
|
|
|
24 --pValue $pValue
|
|
|
25 --fChange $fChange
|
|
|
26 --tool_dir $__tool_directory__
|
|
|
27 --option $cond.type_selector
|
|
|
28 --out_log $log
|
|
|
29 #if $cond.type_selector == 'datasets':
|
|
|
30 --input_datas
|
|
|
31 #for $data in $cond.input_Datasets:
|
|
|
32 ${data.input}
|
|
|
33 #end for
|
|
|
34 --names
|
|
|
35 #for $data in $cond.input_Datasets:
|
|
|
36 ${data.input_name}
|
|
|
37 #end for
|
|
|
38 #elif $cond.type_selector == 'dataset_class':
|
|
|
39 --input_data ${input_data}
|
|
|
40 --input_class ${input_class}
|
|
|
41 #end if
|
|
|
42 ]]>
|
|
|
43 </command>
|
|
1
|
44
|
|
0
|
45 <inputs>
|
|
|
46 <conditional name="cond_rule">
|
|
1
|
47 <expand macro="options" />
|
|
|
48 <when value="HMRcore">
|
|
|
49 </when>
|
|
|
50 <when value="Recon">
|
|
|
51 </when>
|
|
0
|
52 <when value="Custom">
|
|
1
|
53 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
|
|
0
|
54 <conditional name="cond_map">
|
|
|
55 <param name="yes_no" type="select" label="Custom map? (optional)">
|
|
|
56 <option value="no" selected="true">no</option>
|
|
|
57 <option value="yes">yes</option>
|
|
|
58 </param>
|
|
|
59 <when value="yes">
|
|
1
|
60 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
|
|
|
61 </when>
|
|
|
62 <when value="no">
|
|
0
|
63 </when>
|
|
|
64 </conditional>
|
|
|
65 </when>
|
|
|
66 </conditional>
|
|
|
67 <conditional name="cond">
|
|
1
|
68 <param name="type_selector" argument="--option" type="select" label="Input format:">
|
|
|
69 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
|
|
0
|
70 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
|
|
|
71 </param>
|
|
|
72 <when value="datasets">
|
|
|
73 <repeat name="input_Datasets" title="RNAseq" type="data" min="2">
|
|
1
|
74 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
|
|
|
75 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Defalut: Dataset" />
|
|
0
|
76 </repeat>
|
|
|
77 </when>
|
|
|
78 <when value="dataset_class">
|
|
1
|
79 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
|
|
|
80 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
|
|
0
|
81 </when>
|
|
|
82 </conditional>
|
|
1
|
83 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
|
|
|
84 <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold" help="min value 0" />
|
|
|
85 <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold" help="min value 1" />
|
|
0
|
86 </inputs>
|
|
1
|
87
|
|
0
|
88 <outputs>
|
|
1
|
89 <data format="txt" name="log" label="Log" />
|
|
|
90 <collection name="map_svg" type="list" label="Graphical results (.svg)">
|
|
0
|
91 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter>
|
|
1
|
92 <discover_datasets pattern="__name_and_ext__" directory="map_svg" />
|
|
0
|
93 </collection>
|
|
1
|
94 <collection name="map_pdf" type="list" label="Graphical results (.pdf)">
|
|
0
|
95 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter>
|
|
1
|
96 <discover_datasets pattern="__name_and_ext__" directory="map_pdf" />
|
|
0
|
97 </collection>
|
|
1
|
98 <collection name="table_out" type="list" label="Tabular results">
|
|
|
99 <discover_datasets pattern="__name_and_ext__" directory="table_out" />
|
|
0
|
100 </collection>
|
|
|
101 </outputs>
|
|
1
|
102
|
|
|
103
|
|
|
104
|
|
0
|
105 <help>
|
|
|
106 <![CDATA[
|
|
|
107
|
|
|
108 What it does
|
|
|
109 -------------
|
|
|
110
|
|
|
111 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.
|
|
|
112
|
|
1
|
113 Accepted files are:
|
|
|
114 - 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*");
|
|
|
115 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
|
|
|
116
|
|
|
117 Optional files:
|
|
|
118 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
|
|
0
|
119
|
|
1
|
120 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
|
|
|
121 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
|
|
|
122 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
|
|
0
|
123
|
|
1
|
124 The tool generates:
|
|
|
125 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
|
|
|
126 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
|
|
|
127 3) a log file (.txt).
|
|
0
|
128
|
|
1
|
129 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.
|
|
0
|
130
|
|
|
131 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).
|
|
|
132
|
|
|
133 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
|
|
|
134
|
|
1
|
135 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".
|
|
0
|
136
|
|
|
137
|
|
|
138 Example input
|
|
|
139 -------------
|
|
|
140
|
|
1
|
141 **"Custom Rules"** option:
|
|
|
142
|
|
|
143 Custom Rules Dastaset:
|
|
0
|
144
|
|
1
|
145 @CUSTOM_RULES_EXEMPLE@
|
|
|
146
|
|
|
147 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
|
|
0
|
148
|
|
1
|
149 RNA-seq Dataset 1:
|
|
|
150
|
|
|
151 @DATASET_EXEMPLE1@
|
|
0
|
152
|
|
1
|
153 RNA-seq Dataset 2:
|
|
0
|
154
|
|
1
|
155 @DATASET_EXEMPLE2@
|
|
0
|
156
|
|
|
157 **"RNAseq of all samples + sample group specification"** option:
|
|
|
158
|
|
1
|
159 RNA-seq Dataset:
|
|
0
|
160
|
|
1
|
161 @DATASET_EXEMPLE1@
|
|
0
|
162
|
|
|
163 Class-file:
|
|
|
164
|
|
|
165 +------------+------------+
|
|
|
166 | Patient_ID | class |
|
|
|
167 +============+============+
|
|
|
168 | TCGAAA3529 | MSI |
|
|
|
169 +------------+------------+
|
|
|
170 | TCGAA62671 | MSS |
|
|
|
171 +------------+------------+
|
|
|
172 | TCGAA62672 | MSI |
|
|
|
173 +------------+------------+
|
|
|
174
|
|
|
175 |
|
|
|
176
|
|
|
177 .. class:: infomark
|
|
|
178
|
|
1
|
179 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
|
|
0
|
180
|
|
|
181 .. class:: infomark
|
|
|
182
|
|
1
|
183 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
|
|
0
|
184
|
|
1
|
185 @REFERENCE@
|
|
0
|
186
|
|
1
|
187 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
|
|
0
|
188 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
|
|
1
|
189 .. _MaREA cluster analysis: http://link del tool di cluster.org
|
|
0
|
190
|
|
|
191 ]]>
|
|
|
192 </help>
|
|
1
|
193 <expand macro="citations" />
|
|
0
|
194 </tool>
|
|
|
195
|
