|
63
|
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.8">
|
|
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}
|
|
63
|
31 #if $cond.advanced.cond_map == 'true':
|
|
|
32 --custom_rules true
|
|
|
33 --custom_rule ${cond.advanced.cond_map.custom_rule}
|
|
|
34 --custom_map ${cond.advanced.cond_map.custom_map}
|
|
|
35 #end if
|
|
31
|
36 #if $cond.advanced.choice == 'true':
|
|
47
|
37 --pValue ${cond.advanced.pValue}
|
|
|
38 --fChange ${cond.advanced.fChange}
|
|
|
39 --generate_svg ${cond.advanced.generateSvg}
|
|
|
40 --generate_pdf ${cond.advanced.generatePdf}
|
|
|
41 #else
|
|
|
42 --pValue 0.05
|
|
|
43 --fChange 1.5
|
|
|
44 --generate_svg false
|
|
|
45 --generate_pdf true
|
|
|
46 --generate_ras false
|
|
|
47 #end if
|
|
16
|
48 #elif $cond.type_selector == 'dataset_class':
|
|
|
49 --input_data ${input_data}
|
|
|
50 --input_class ${input_class}
|
|
47
|
51 --comparison ${cond.comparis.comparison}
|
|
|
52 #if $cond.comparis.comparison == 'onevsmany'
|
|
|
53 --control ${cond.comparis.controlgroup}
|
|
|
54 #end if
|
|
63
|
55 #if $cond.advanced.cond_map == 'true':
|
|
|
56 --custom_rules true
|
|
|
57 --custom_rule ${cond.advanced.cond_map.custom_rule}
|
|
|
58 --custom_map ${cond.advanced.cond_map.custom_map}
|
|
|
59 #end if
|
|
31
|
60 #if $cond.advanced.choice == 'true':
|
|
47
|
61 --pValue ${cond.advanced.pValue}
|
|
|
62 --fChange ${cond.advanced.fChange}
|
|
|
63 --generate_svg ${cond.advanced.generateSvg}
|
|
|
64 --generate_pdf ${cond.advanced.generatePdf}
|
|
|
65 #else
|
|
|
66 --pValue 0.05
|
|
|
67 --fChange 1.5
|
|
|
68 --generate_svg false
|
|
|
69 --generate_pdf true
|
|
|
70 #end if
|
|
28
|
71 #end if
|
|
16
|
72 ]]>
|
|
47
|
73 </command>
|
|
|
74 <inputs>
|
|
|
75 <conditional name="cond">
|
|
|
76 <param name="type_selector" argument="--option" type="select" label="Input format:">
|
|
|
77 <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
|
|
|
78 <option value="dataset_class">RAS of all samples + sample group specification</option>
|
|
|
79 </param>
|
|
|
80 <when value="datasets">
|
|
|
81 <repeat name="input_Datasets" title="RAS dataset" min="2">
|
|
|
82 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
|
|
|
83 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
|
|
|
84 </repeat>
|
|
|
85 <conditional name="comparis">
|
|
|
86 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
|
|
|
87 <option value="manyvsmany" selected="true">One vs One</option>
|
|
|
88 <option value="onevsrest">One vs All</option>
|
|
|
89 <option value="onevsmany">One vs Control</option>
|
|
|
90 </param>
|
|
|
91 <when value="onevsmany">
|
|
|
92 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
|
|
|
93 </when>
|
|
|
94 </conditional>
|
|
|
95 <conditional name="advanced">
|
|
33
|
96 <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
|
97 <option value="true" selected="true">No</option>
|
|
|
98 <option value="false">Yes</option>
|
|
31
|
99 </param>
|
|
47
|
100 <when value="false"></when>
|
|
31
|
101 <when value="true">
|
|
47
|
102 <conditional name="cond_map">
|
|
63
|
103 <param name="choice" type="boolean" checked="false" label="Use custom map and rules?" help="Use this option only if you have generated RAS using a custom set of rules">
|
|
47
|
104 <option value="false" selected="true">No</option>
|
|
|
105 <option value="true">Yes</option>
|
|
|
106 </param>
|
|
63
|
107 <when value="true">
|
|
|
108 <param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
|
|
47
|
109 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
|
|
|
110 </when>
|
|
|
111 </conditional>
|
|
|
112 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
|
|
|
113 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
|
|
|
114 <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?" />
|
|
|
115 <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
|
116 </when>
|
|
47
|
117 </conditional>
|
|
|
118 </when>
|
|
|
119 <when value="dataset_class">
|
|
|
120 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
|
|
16
|
121 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
|
|
47
|
122 <conditional name="comparis">
|
|
|
123 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
|
|
|
124 <option value="manyvsmany" selected="true">One vs One</option>
|
|
|
125 <option value="onevsrest">One vs All</option>
|
|
|
126 <option value="onevsmany">One vs Control</option>
|
|
31
|
127 </param>
|
|
47
|
128 <when value="onevsmany">
|
|
|
129 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
|
|
31
|
130 </when>
|
|
47
|
131 </conditional>
|
|
|
132 <conditional name="advanced">
|
|
|
133 <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.">
|
|
|
134 <option value="true" selected="true">No</option>
|
|
|
135 <option value="false">Yes</option>
|
|
|
136 </param>
|
|
|
137 <when value="false"></when>
|
|
|
138 <when value="true">
|
|
|
139 <conditional name="cond_map">
|
|
63
|
140 <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
|
141 <option value="false" selected="true">No</option>
|
|
|
142 <option value="true">Yes</option>
|
|
|
143 </param>
|
|
63
|
144 <when value="true">
|
|
|
145 <param name="Custom_rule" argument="--custom_rule" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
|
|
|
146 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
|
|
47
|
147 </when>
|
|
|
148 </conditional>
|
|
|
149 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
|
|
|
150 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
|
|
|
151 <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?" />
|
|
|
152 <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?" />
|
|
|
153 </when>
|
|
|
154 </conditional>
|
|
|
155 </when>
|
|
|
156 </conditional>
|
|
|
157 </inputs>
|
|
|
158 <outputs>
|
|
|
159 <data format="txt" name="log" label="MaREA - Log" />
|
|
|
160 <collection name="results" type="list" label="MaREA - Results">
|
|
|
161 <discover_datasets pattern="__name_and_ext__" directory="result"/>
|
|
16
|
162 </collection>
|
|
47
|
163 </outputs>
|
|
|
164 <help>
|
|
|
165 <![CDATA[
|
|
16
|
166
|
|
|
167 What it does
|
|
|
168 -------------
|
|
|
169
|
|
48
|
170 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
|
171
|
|
33
|
172 Accepted files are:
|
|
48
|
173 - 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");
|
|
|
174 - option 2) one RAS dataset and one group-file specifying the group each sample belongs to.
|
|
|
175
|
|
|
176 RAS datasets format: tab-separated text files, reporting the RAS value of each reaction (row) for a given sample (column).
|
|
|
177
|
|
|
178 Column header: sample ID.
|
|
|
179 Raw header: reaction ID.
|
|
16
|
180
|
|
|
181 Optional files:
|
|
|
182 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
|
|
|
183
|
|
|
184 The tool generates:
|
|
48
|
185 - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
|
|
|
186 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
|
|
|
187 - 3) a log file (.txt).
|
|
|
188
|
|
|
189 Output options:
|
|
|
190 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
|
191
|
|
48
|
192 Alternative options are:
|
|
|
193 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
|
|
|
194 - 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
|
195
|
|
|
196 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".
|
|
|
197
|
|
|
198 Example input
|
|
|
199 -------------
|
|
|
200
|
|
48
|
201 "RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
|
|
16
|
202
|
|
48
|
203 RAS Dataset 1:
|
|
16
|
204
|
|
48
|
205 +------------+----------------+----------------+----------------+
|
|
|
206 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
|
|
|
207 +============+================+================+================+
|
|
|
208 | r1642 | 0.523167 | 0.371355 | 0.925661 |
|
|
|
209 +------------+----------------+----------------+----------------+
|
|
|
210 | r1643 | 0.568765 | 0.765567 | 0.456789 |
|
|
|
211 +------------+----------------+----------------+----------------+
|
|
|
212 | r1640 | 0.876545 | 0.768933 | 0.987654 |
|
|
|
213 +------------+----------------+----------------+----------------+
|
|
|
214 | r1641 | 0.456788 | 0.876543 | 0.876542 |
|
|
|
215 +------------+----------------+----------------+----------------+
|
|
|
216 | r1646 | 0.876543 | 0.786543 | 0.897654 |
|
|
|
217 +------------+----------------+----------------+----------------+
|
|
16
|
218
|
|
48
|
219 RAS Dataset 2:
|
|
16
|
220
|
|
48
|
221 +------------+----------------+----------------+----------------+
|
|
|
222 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
|
|
|
223 +============+================+================+================+
|
|
|
224 | r1642 | 0.523167 | 0.371355 | 0.925661 |
|
|
|
225 +------------+----------------+----------------+----------------+
|
|
|
226 | r1643 | 0.568765 | 0.765567 | 0.456789 |
|
|
|
227 +------------+----------------+----------------+----------------+
|
|
|
228 | r1640 | 0.876545 | 0.768933 | 0.987654 |
|
|
|
229 +------------+----------------+----------------+----------------+
|
|
|
230 | r1641 | 0.456788 | 0.876543 | 0.876542 |
|
|
|
231 +------------+----------------+----------------+----------------+
|
|
|
232 | r1646 | 0.876543 | 0.786543 | 0.897654 |
|
|
|
233 +------------+----------------+----------------+----------------+
|
|
16
|
234
|
|
48
|
235 "RAS of all samples + sample group specification" option:
|
|
16
|
236
|
|
48
|
237 RAS Dataset:
|
|
16
|
238
|
|
48
|
239 +------------+----------------+----------------+----------------+
|
|
|
240 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
|
|
|
241 +============+================+================+================+
|
|
|
242 | r1642 | 0.523167 | 0.371355 | 0.925661 |
|
|
|
243 +------------+----------------+----------------+----------------+
|
|
|
244 | r1643 | 0.568765 | 0.765567 | 0.456789 |
|
|
|
245 +------------+----------------+----------------+----------------+
|
|
|
246 | r1640 | 0.876545 | 0.768933 | 0.987654 |
|
|
|
247 +------------+----------------+----------------+----------------+
|
|
|
248 | r1641 | 0.456788 | 0.876543 | 0.876542 |
|
|
|
249 +------------+----------------+----------------+----------------+
|
|
|
250 | r1646 | 0.876543 | 0.786543 | 0.897654 |
|
|
|
251 +------------+----------------+----------------+----------------+
|
|
16
|
252
|
|
48
|
253 Group-file
|
|
16
|
254
|
|
48
|
255 +---------------+-----------+
|
|
|
256 | Patient ID | Class |
|
|
|
257 +===============+===========+
|
|
|
258 | TCGAAA3529 | MSI |
|
|
|
259 +---------------+-----------+
|
|
|
260 | TCGAA62671 | MSS |
|
|
|
261 +---------------+-----------+
|
|
|
262 | TCGAA62672 | MSI |
|
|
|
263 +---------------+-----------+
|
|
16
|
264
|
|
48
|
265 Advanced options
|
|
|
266 ----------------
|
|
|
267
|
|
|
268 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
|
|
|
269
|
|
|
270 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;
|
|
|
271
|
|
16
|
272
|
|
|
273 .. class:: infomark
|
|
|
274
|
|
|
275 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
|
|
|
276
|
|
|
277 .. class:: infomark
|
|
|
278
|
|
|
279 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
|
|
|
280
|
|
|
281 @REFERENCE@
|
|
|
282
|
|
|
283 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
|
|
|
284 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
|
|
|
285 .. _MaREA cluster analysis: http://link del tool di cluster.org
|
|
|
286
|
|
|
287 ]]>
|
|
47
|
288 </help>
|
|
|
289 <expand macro="citations" />undefined</tool>
|
|
33
|
290
|
