|
57
|
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.1.0">
|
|
47
|
2 <macros>
|
|
|
3 <import>marea_macros.xml</import>
|
|
|
4 </macros>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="0.23.0">pandas</requirement>
|
|
|
7 <requirement type="package" version="1.1.0">scipy</requirement>
|
|
|
8 <requirement type="package" version="0.10.1">cobra</requirement>
|
|
|
9 <requirement type="package" version="4.2.1">lxml</requirement>
|
|
|
10 <requirement type="package" version="0.8.1">svglib</requirement>
|
|
|
11 <requirement type="package" version="3.4.0">reportlab</requirement>
|
|
|
12 </requirements>
|
|
|
13 <command detect_errors="exit_code">
|
|
|
14 <![CDATA[
|
|
16
|
15 python $__tool_directory__/marea.py
|
|
47
|
16
|
|
16
|
17 --tool_dir $__tool_directory__
|
|
|
18 --option $cond.type_selector
|
|
33
|
19 --out_log $log
|
|
|
20
|
|
16
|
21 #if $cond.type_selector == 'datasets':
|
|
|
22 --input_datas
|
|
|
23 #for $data in $cond.input_Datasets:
|
|
|
24 ${data.input}
|
|
|
25 #end for
|
|
|
26 --names
|
|
|
27 #for $data in $cond.input_Datasets:
|
|
|
28 ${data.input_name}
|
|
|
29 #end for
|
|
47
|
30 --comparison ${cond.comparis.comparison}
|
|
48
|
31 #if $cond.advanced.cond_map == 'true':
|
|
|
32 --custom_rules true
|
|
|
33 --custom_map ${cond.advanced.cond_map.custom_map}
|
|
|
34 #end if
|
|
31
|
35 #if $cond.advanced.choice == 'true':
|
|
47
|
36 --pValue ${cond.advanced.pValue}
|
|
|
37 --fChange ${cond.advanced.fChange}
|
|
|
38 --generate_svg ${cond.advanced.generateSvg}
|
|
|
39 --generate_pdf ${cond.advanced.generatePdf}
|
|
|
40 #else
|
|
|
41 --pValue 0.05
|
|
|
42 --fChange 1.5
|
|
|
43 --generate_svg false
|
|
|
44 --generate_pdf true
|
|
|
45 --generate_ras false
|
|
|
46 #end if
|
|
16
|
47 #elif $cond.type_selector == 'dataset_class':
|
|
|
48 --input_data ${input_data}
|
|
|
49 --input_class ${input_class}
|
|
47
|
50 --comparison ${cond.comparis.comparison}
|
|
|
51 #if $cond.comparis.comparison == 'onevsmany'
|
|
|
52 --control ${cond.comparis.controlgroup}
|
|
|
53 #end if
|
|
48
|
54 #if $cond.advanced.cond_map == 'true':
|
|
|
55 --custom_rules true
|
|
|
56 --custom_map ${cond.advanced.cond_map.custom_map}
|
|
|
57 #end if
|
|
31
|
58 #if $cond.advanced.choice == 'true':
|
|
47
|
59 --pValue ${cond.advanced.pValue}
|
|
|
60 --fChange ${cond.advanced.fChange}
|
|
|
61 --generate_svg ${cond.advanced.generateSvg}
|
|
|
62 --generate_pdf ${cond.advanced.generatePdf}
|
|
|
63 #else
|
|
|
64 --pValue 0.05
|
|
|
65 --fChange 1.5
|
|
|
66 --generate_svg false
|
|
|
67 --generate_pdf true
|
|
|
68 #end if
|
|
28
|
69 #end if
|
|
16
|
70 ]]>
|
|
47
|
71 </command>
|
|
|
72 <inputs>
|
|
|
73 <conditional name="cond">
|
|
|
74 <param name="type_selector" argument="--option" type="select" label="Input format:">
|
|
|
75 <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
|
|
|
76 <option value="dataset_class">RAS of all samples + sample group specification</option>
|
|
|
77 </param>
|
|
|
78 <when value="datasets">
|
|
|
79 <repeat name="input_Datasets" title="RAS dataset" min="2">
|
|
|
80 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
|
|
|
81 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
|
|
|
82 </repeat>
|
|
|
83 <conditional name="comparis">
|
|
|
84 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
|
|
|
85 <option value="manyvsmany" selected="true">One vs One</option>
|
|
|
86 <option value="onevsrest">One vs All</option>
|
|
|
87 <option value="onevsmany">One vs Control</option>
|
|
|
88 </param>
|
|
|
89 <when value="onevsmany">
|
|
|
90 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
|
|
|
91 </when>
|
|
|
92 </conditional>
|
|
|
93 <conditional name="advanced">
|
|
33
|
94 <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
|
|
47
|
95 <option value="true" selected="true">No</option>
|
|
|
96 <option value="false">Yes</option>
|
|
31
|
97 </param>
|
|
47
|
98 <when value="false"></when>
|
|
31
|
99 <when value="true">
|
|
47
|
100 <conditional name="cond_map">
|
|
55
|
101 <param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
|
|
47
|
102 <option value="false" selected="true">No</option>
|
|
|
103 <option value="true">Yes</option>
|
|
|
104 </param>
|
|
55
|
105 <when value="true">
|
|
47
|
106 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
|
|
|
107 </when>
|
|
|
108 </conditional>
|
|
|
109 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
|
|
|
110 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
|
|
|
111 <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />
|
|
|
112 <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" />
|
|
31
|
113 </when>
|
|
47
|
114 </conditional>
|
|
|
115 </when>
|
|
|
116 <when value="dataset_class">
|
|
|
117 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
|
|
16
|
118 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
|
|
47
|
119 <conditional name="comparis">
|
|
|
120 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
|
|
|
121 <option value="manyvsmany" selected="true">One vs One</option>
|
|
|
122 <option value="onevsrest">One vs All</option>
|
|
|
123 <option value="onevsmany">One vs Control</option>
|
|
31
|
124 </param>
|
|
47
|
125 <when value="onevsmany">
|
|
|
126 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
|
|
31
|
127 </when>
|
|
47
|
128 </conditional>
|
|
|
129 <conditional name="advanced">
|
|
|
130 <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
|
|
|
131 <option value="true" selected="true">No</option>
|
|
|
132 <option value="false">Yes</option>
|
|
|
133 </param>
|
|
|
134 <when value="false"></when>
|
|
|
135 <when value="true">
|
|
|
136 <conditional name="cond_map">
|
|
|
137 <param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules">
|
|
|
138 <option value="false" selected="true">No</option>
|
|
|
139 <option value="true">Yes</option>
|
|
|
140 </param>
|
|
57
|
141 <when value="true">
|
|
47
|
142 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
|
|
|
143 </when>
|
|
|
144 </conditional>
|
|
|
145 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
|
|
|
146 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
|
|
|
147 <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />
|
|
|
148 <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" />
|
|
|
149 </when>
|
|
|
150 </conditional>
|
|
|
151 </when>
|
|
|
152 </conditional>
|
|
|
153 </inputs>
|
|
|
154 <outputs>
|
|
|
155 <data format="txt" name="log" label="MaREA - Log" />
|
|
|
156 <collection name="results" type="list" label="MaREA - Results">
|
|
|
157 <discover_datasets pattern="__name_and_ext__" directory="result"/>
|
|
16
|
158 </collection>
|
|
47
|
159 </outputs>
|
|
|
160 <help>
|
|
|
161 <![CDATA[
|
|
16
|
162
|
|
|
163 What it does
|
|
|
164 -------------
|
|
|
165
|
|
48
|
166 This tool analyzes and visualizes differences in the Reaction Activity Scores (RASs) of groups of samples, as computed by the Expression2RAS tool, of groups of samples.
|
|
16
|
167
|
|
33
|
168 Accepted files are:
|
|
48
|
169 - option 1) two or more RAS datasets, each referring to samples in a given group. The user can specify a label for each group (as e.g. "classA" and "classB");
|
|
|
170 - option 2) one RAS dataset and one group-file specifying the group each sample belongs to.
|
|
|
171
|
|
|
172 RAS datasets format: tab-separated text files, reporting the RAS value of each reaction (row) for a given sample (column).
|
|
|
173
|
|
|
174 Column header: sample ID.
|
|
|
175 Raw header: reaction ID.
|
|
16
|
176
|
|
|
177 Optional files:
|
|
|
178 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
|
|
|
179
|
|
|
180 The tool generates:
|
|
48
|
181 - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
|
|
|
182 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
|
|
|
183 - 3) a log file (.txt).
|
|
|
184
|
|
|
185 Output options:
|
|
|
186 To calculate P-Values and Fold-Changes and to enrich maps, comparisons are performed for each possible pair of groups (default option ‘One vs One’).
|
|
16
|
187
|
|
48
|
188 Alternative options are:
|
|
|
189 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
|
|
|
190 - comparison of each group vs. a control group (option ‘One vs Control). If this option is selected the user must indicate the control group label.
|
|
16
|
191
|
|
|
192 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".
|
|
|
193
|
|
|
194 Example input
|
|
|
195 -------------
|
|
|
196
|
|
48
|
197 "RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
|
|
16
|
198
|
|
48
|
199 RAS Dataset 1:
|
|
16
|
200
|
|
48
|
201 +------------+----------------+----------------+----------------+
|
|
|
202 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
|
|
|
203 +============+================+================+================+
|
|
|
204 | r1642 | 0.523167 | 0.371355 | 0.925661 |
|
|
|
205 +------------+----------------+----------------+----------------+
|
|
|
206 | r1643 | 0.568765 | 0.765567 | 0.456789 |
|
|
|
207 +------------+----------------+----------------+----------------+
|
|
|
208 | r1640 | 0.876545 | 0.768933 | 0.987654 |
|
|
|
209 +------------+----------------+----------------+----------------+
|
|
|
210 | r1641 | 0.456788 | 0.876543 | 0.876542 |
|
|
|
211 +------------+----------------+----------------+----------------+
|
|
|
212 | r1646 | 0.876543 | 0.786543 | 0.897654 |
|
|
|
213 +------------+----------------+----------------+----------------+
|
|
16
|
214
|
|
48
|
215 RAS Dataset 2:
|
|
16
|
216
|
|
48
|
217 +------------+----------------+----------------+----------------+
|
|
|
218 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
|
|
|
219 +============+================+================+================+
|
|
|
220 | r1642 | 0.523167 | 0.371355 | 0.925661 |
|
|
|
221 +------------+----------------+----------------+----------------+
|
|
|
222 | r1643 | 0.568765 | 0.765567 | 0.456789 |
|
|
|
223 +------------+----------------+----------------+----------------+
|
|
|
224 | r1640 | 0.876545 | 0.768933 | 0.987654 |
|
|
|
225 +------------+----------------+----------------+----------------+
|
|
|
226 | r1641 | 0.456788 | 0.876543 | 0.876542 |
|
|
|
227 +------------+----------------+----------------+----------------+
|
|
|
228 | r1646 | 0.876543 | 0.786543 | 0.897654 |
|
|
|
229 +------------+----------------+----------------+----------------+
|
|
16
|
230
|
|
48
|
231 "RAS of all samples + sample group specification" option:
|
|
16
|
232
|
|
48
|
233 RAS Dataset:
|
|
16
|
234
|
|
48
|
235 +------------+----------------+----------------+----------------+
|
|
|
236 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
|
|
|
237 +============+================+================+================+
|
|
|
238 | r1642 | 0.523167 | 0.371355 | 0.925661 |
|
|
|
239 +------------+----------------+----------------+----------------+
|
|
|
240 | r1643 | 0.568765 | 0.765567 | 0.456789 |
|
|
|
241 +------------+----------------+----------------+----------------+
|
|
|
242 | r1640 | 0.876545 | 0.768933 | 0.987654 |
|
|
|
243 +------------+----------------+----------------+----------------+
|
|
|
244 | r1641 | 0.456788 | 0.876543 | 0.876542 |
|
|
|
245 +------------+----------------+----------------+----------------+
|
|
|
246 | r1646 | 0.876543 | 0.786543 | 0.897654 |
|
|
|
247 +------------+----------------+----------------+----------------+
|
|
16
|
248
|
|
48
|
249 Group-file
|
|
16
|
250
|
|
48
|
251 +---------------+-----------+
|
|
|
252 | Patient ID | Class |
|
|
|
253 +===============+===========+
|
|
|
254 | TCGAAA3529 | MSI |
|
|
|
255 +---------------+-----------+
|
|
|
256 | TCGAA62671 | MSS |
|
|
|
257 +---------------+-----------+
|
|
|
258 | TCGAA62672 | MSI |
|
|
|
259 +---------------+-----------+
|
|
16
|
260
|
|
48
|
261 Advanced options
|
|
|
262 ----------------
|
|
|
263
|
|
|
264 P-Value threshold: the threshold used for significance Kolmogorov-Smirnov (KS) test, to verify whether the distributions of RASs over the samples in two sets are significantly different
|
|
|
265
|
|
|
266 Fold-Change threshold: threshold of the fold-change between the average RAS of two groups. Among the reactions that pass the KS test, only fold-change values larger than the indicated threshold will be visualized on the output metabolic map;
|
|
|
267
|
|
16
|
268
|
|
|
269 .. class:: infomark
|
|
|
270
|
|
|
271 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
|
|
|
272
|
|
|
273 .. class:: infomark
|
|
|
274
|
|
|
275 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
|
|
|
276
|
|
|
277 @REFERENCE@
|
|
|
278
|
|
|
279 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
|
|
|
280 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
|
|
|
281 .. _MaREA cluster analysis: http://link del tool di cluster.org
|
|
|
282
|
|
|
283 ]]>
|
|
47
|
284 </help>
|
|
|
285 <expand macro="citations" />undefined</tool>
|
|
33
|
286
|
