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author bimib
date Wed, 07 Nov 2018 07:07:46 -0500
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1 <tool id="MaREA" name="Metabolic Enrichment Analysis"> 1 <tool id="MaREA" name="Metabolic Enrichment Analysis">
2 <description>for Galaxy</description> 2 <description>for Galaxy</description>
3 <macros>
4 <import>marea_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
3 <requirements> 7 <requirements>
4 <requirement type="package">pandas</requirement>
5 <requirement type="package">scipy</requirement>
6 <requirement type="package">lxml</requirement> 8 <requirement type="package">lxml</requirement>
7 <requirement type="package">svglib</requirement> 9 <requirement type="package">svglib</requirement>
8 <requirement type="package">reportlab</requirement> 10 <requirement type="package">reportlab</requirement>
9 <requirement type="package">cobrapy</requirement>
10 <requirement type="package">python-libsbml</requirement>
11 </requirements> 11 </requirements>
12 <command> 12 <command detect_errors="exit_code">
13 <![CDATA[ 13 <![CDATA[
14 python $__tool_directory__/marea.py 14 python $__tool_directory__/marea.py
15 --rules_selector $cond_rule.rules_selector 15 --rules_selector $cond_rule.rules_selector
16 #if $cond_rule.rules_selector == 'Custom': 16 #if $cond_rule.rules_selector == 'Custom':
17 --custom ${cond_rule.Custom_rules} 17 --custom ${cond_rule.Custom_rules}
39 --input_data ${input_data} 39 --input_data ${input_data}
40 --input_class ${input_class} 40 --input_class ${input_class}
41 #end if 41 #end if
42 ]]> 42 ]]>
43 </command> 43 </command>
44
44 <inputs> 45 <inputs>
45 <conditional name="cond_rule"> 46 <conditional name="cond_rule">
46 <param name="rules_selector" type="select" label="Gene-Protein-Reaction rules:"> 47 <expand macro="options" />
47 <option value="HMRcore" selected="true">HMRcore rules</option> 48 <when value="HMRcore">
48 <option value="Recon">Recon 2.2 rules</option> 49 </when>
49 <option value="Custom">Custom rules</option> 50 <when value="Recon">
50 </param> 51 </when>
51 <when value="Custom"> 52 <when value="Custom">
52 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules"/> 53 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
53 <conditional name="cond_map"> 54 <conditional name="cond_map">
54 <param name="yes_no" type="select" label="Custom map? (optional)"> 55 <param name="yes_no" type="select" label="Custom map? (optional)">
55 <option value="no" selected="true">no</option> 56 <option value="no" selected="true">no</option>
56 <option value="yes">yes</option> 57 <option value="yes">yes</option>
57 </param> 58 </param>
58 <when value="yes"> 59 <when value="yes">
59 <param name="Custom_map" type="data" format="xml, svg" label="custom-map.svg"/> 60 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
61 </when>
62 <when value="no">
60 </when> 63 </when>
61 </conditional> 64 </conditional>
62 </when> 65 </when>
63 </conditional> 66 </conditional>
64 <conditional name="cond"> 67 <conditional name="cond">
65 <param name="type_selector" type="select" label="Input format:"> 68 <param name="type_selector" argument="--option" type="select" label="Input format:">
66 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + … + RNAseq of group N</option> 69 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
67 <option value="dataset_class">RNAseq of all samples + sample group specification</option> 70 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
68 </param> 71 </param>
69 <when value="datasets"> 72 <when value="datasets">
70 <repeat name="input_Datasets" title="RNAseq" type="data" min="2"> 73 <repeat name="input_Datasets" title="RNAseq" type="data" min="2">
71 <param name="input" type="data" format="tabular, csv, tsv" label="add dataset"/> 74 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
72 <param name="input_name" type="text" label="Dataset's name:" value="Dataset" help="Defalut: Dataset"/> 75 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Defalut: Dataset" />
73 </repeat> 76 </repeat>
74 </when> 77 </when>
75 <when value="dataset_class"> 78 <when value="dataset_class">
76 <param name="input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples"/> 79 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
77 <param name="input_class" type="data" format="tabular, csv, tsv" label="Sample group specification"/> 80 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
78 </when> 81 </when>
79 </conditional> 82 </conditional>
80 <param name="None" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?"/> 83 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
81 <param name="pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold" help="min value 0"/> 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" />
82 <param name="fChange" type="float" size="20" value="1.5" min="1" label="Fold-Cahnge threshold" help="min value 1"/> 85 <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold" help="min value 1" />
83 </inputs> 86 </inputs>
87
84 <outputs> 88 <outputs>
85 <data format="txt" name="log" label="Log"/> 89 <data format="txt" name="log" label="Log" />
86 <collection name="map_svg" type="list" label="file svg"> 90 <collection name="map_svg" type="list" label="Graphical results (.svg)">
87 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter> 91 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter>
88 <discover_datasets pattern="__name_and_ext__" directory="map_svg"/> 92 <discover_datasets pattern="__name_and_ext__" directory="map_svg" />
89 </collection> 93 </collection>
90 <collection name="map_pdf" type="list" label="file pdf"> 94 <collection name="map_pdf" type="list" label="Graphical results (.pdf)">
91 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter> 95 <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter>
92 <discover_datasets pattern="__name_and_ext__" directory="map_pdf"/> 96 <discover_datasets pattern="__name_and_ext__" directory="map_pdf" />
93 </collection> 97 </collection>
94 <collection name="table_out" type="list" label="file table"> 98 <collection name="table_out" type="list" label="Tabular results">
95 <discover_datasets pattern="__name_and_ext__" directory="table_out"/> 99 <discover_datasets pattern="__name_and_ext__" directory="table_out" />
96 </collection> 100 </collection>
97 </outputs> 101 </outputs>
102
103
104
98 <help> 105 <help>
99 <![CDATA[ 106 <![CDATA[
100 107
101 What it does 108 What it does
102 ------------- 109 -------------
103 110
104 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. 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.
105 112
106 The tool can be used to generate: 113 Accepted files are:
107 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes 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*");
108 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes 115 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
109 3) a log file (.txt)
110 116
111 Accepted files are: 117 Optional files:
112 1) or 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”). 118 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
113 2) or one RNA dataset and one class-file specifying the class/condition each sample belongs to.
114 119
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.
115 123
116 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. 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).
128
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.
117 130
118 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). 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).
119 132
120 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes. 133 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
121 134
122 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”. 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".
123
124 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
125 136
126 137
127 Example input 138 Example input
128 ------------- 139 -------------
129 140
130 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N" exemple input"** option: 141 **"Custom Rules"** option:
131 142
132 Dataset 1: 143 Custom Rules Dastaset:
133 144
134 +------------+------------+------------+------------+ 145 @CUSTOM_RULES_EXEMPLE@
135 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
136 +============+============+============+============+
137 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
138 +------------+------------+------------+------------+
139 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
140 +------------+------------+------------+------------+
141 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
142 +------------+------------+------------+------------+
143 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
144 +------------+------------+------------+------------+
145 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
146 +------------+------------+------------+------------+
147
148 |
149 146
150 Dataset 2: 147 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
151 148
152 +-------------+------------+------------+------------+ 149 RNA-seq Dataset 1:
153 | Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
154 +=============+============+============+============+
155 | A1BG | 0.523167 | 0.371355 | 0.925661 |
156 +-------------+------------+------------+------------+
157 | A1CF | 0.568765 | 0.765567 | 0.456789 |
158 +-------------+------------+------------+------------+
159 | A2M | 0.876545 | 0.768933 | 0.987654 |
160 +-------------+------------+------------+------------+
161 | A4GALT | 0.456788 | 0.876543 | 0.876542 |
162 +-------------+------------+------------+------------+
163 | M664Y65 | 0.876543 | 0.786543 | 0.897654 |
164 +-------------+------------+------------+------------+
165 150
166 | 151 @DATASET_EXEMPLE1@
152
153 RNA-seq Dataset 2:
154
155 @DATASET_EXEMPLE2@
167 156
168 **"RNAseq of all samples + sample group specification"** option: 157 **"RNAseq of all samples + sample group specification"** option:
169 158
170 Dataset: 159 RNA-seq Dataset:
171 160
172 +------------+------------+------------+------------+ 161 @DATASET_EXEMPLE1@
173 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
174 +============+============+============+============+
175 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
176 +------------+------------+------------+------------+
177 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
178 +------------+------------+------------+------------+
179 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
180 +------------+------------+------------+------------+
181 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
182 +------------+------------+------------+------------+
183 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
184 +------------+------------+------------+------------+
185
186 |
187 162
188 Class-file: 163 Class-file:
189 164
190 +------------+------------+ 165 +------------+------------+
191 | Patient_ID | class | 166 | Patient_ID | class |
197 | TCGAA62672 | MSI | 172 | TCGAA62672 | MSI |
198 +------------+------------+ 173 +------------+------------+
199 174
200 | 175 |
201 176
177 .. class:: infomark
202 178
203 179 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
204 .. class:: warningmark
205
206 This tool expects input datasets consisting of tab-delimited columns.
207
208 180
209 .. class:: infomark 181 .. class:: infomark
210 182
211 TIP: If your data is not TAB delimited, use `Convert delimiters to TAB`_. 183 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
212 184
213 .. class:: infomark 185 @REFERENCE@
214 186
215 TIP: If your dataset is not split into classes, use `Cluster for MaREA`_. 187 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
216
217 This tool is developed by the `nome del gruppo di bioinformatica`_ at the `dipartimento di informatica disco`_.
218
219
220 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj 188 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
221 .. _Cluster for MaREA: http://link del tool di cluster.org/ 189 .. _MaREA cluster analysis: http://link del tool di cluster.org
222 .. _nome del gruppo di bioinformatica: http://sito di bio.org
223 .. _dipartimento di informatica disco : http://www.disco.unimib.it/go/Home/English
224 190
225 ]]> 191 ]]>
226 </help> 192 </help>
193 <expand macro="citations" />
227 </tool> 194 </tool>
228 195
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