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date Sun, 13 Oct 2024 11:41:34 +0000
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1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="2.0.0">
2 <macros>
3 <import>marea_macros.xml</import>
4 </macros>
5
6 <requirements>
7 <requirement type="package" version="1.24.4">numpy</requirement>
8 <requirement type="package" version="2.0.3">pandas</requirement>
9 <requirement type="package" version="5.2.2">lxml</requirement>
10 <requirement type="package" version="1.10.1">scipy</requirement>
11 <requirement type="package" version="1.5.1">svglib</requirement>
12 <requirement type="package" version="2.2.3">pyvips</requirement>
13 <requirement type="package" version="2.7.1">cairosvg</requirement>
14 <requirement type="package" version="0.29.0">cobra</requirement>
15 </requirements>
16
17 <command detect_errors="exit_code">
18 <![CDATA[
19 python $__tool_directory__/marea.py
20
21 --tool_dir $__tool_directory__
22 --option $cond.type_selector
23 --out_log $log
24
25 #if $cond.type_selector == 'datasets':
26
27 --using_RAS $cond.using_ras.check
28 --using_RPS $cond.using_rps.check
29
30 #if $cond.using_ras.check == 'true':
31 --input_datas
32 #for $data in $cond.using_ras.input_datasets:
33 ${data.input}
34 #end for
35
36 --names
37 #for $data in $cond.using_ras.input_datasets:
38 ${data.input_name}
39 #end for
40 #end if
41
42 #if $cond.using_rps.check == 'true':
43 --input_datas_rps
44 #for $data in $cond.using_rps.input_datasets_rps:
45 ${data.input_rps}
46 #end for
47
48 --names_rps
49 #for $data in $cond.using_rps.input_datasets_rps:
50 ${data.input_name_rps}
51 #end for
52 #end if
53
54 #elif $cond.type_selector == 'dataset_class':
55
56 --using_RAS $cond.using_ras_all.check
57 --using_RPS $cond.using_rps_all.check
58
59 #if $cond.using_ras_all.check == 'true':
60 --input_data ${cond.using_ras_all.input_data}
61 --input_class ${cond.using_ras_all.input_class}
62 #end if
63
64 #if $cond.using_rps_all.check == 'true':
65 --input_data_rps ${cond.using_rps_all.input_data_rps}
66 --input_class_rps ${cond.using_rps_all.input_class_rps}
67 #end if
68 #end if
69
70 --comparison ${comparis.comparison}
71 #if $comparis.comparison == 'onevsmany'
72 --control '${cond.comparis.controlgroup}'
73 #end if
74
75 --choice_map '${cond_choice_map.choice_map}'
76 #if $cond_choice_map.choice_map == 'Custom':
77 --custom_map ${cond_choice_map.custom_map}
78 #end if
79
80 #if $advanced.choice == 'true':
81 --pValue ${advanced.pValue}
82 --fChange ${advanced.fChange}
83 --generate_svg ${advanced.generateSvg}
84 --generate_pdf ${advanced.generatePdf}
85 --net ${advanced.netRPS}
86 #else
87 --pValue 0.05
88 --fChange 1.2
89 --generate_svg false
90 --generate_pdf true
91 --net false
92 #end if
93 ]]>
94 </command>
95
96 <inputs>
97 <conditional name="cond">
98 <param name="type_selector" argument="--option" type="select" label="Input format:">
99 <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option>
100 <option value="dataset_class">RAS of all samples + sample group specification</option>
101 </param>
102
103 <when value="datasets">
104 <conditional name = "using_ras">
105 <param name = "check" argument = "--using_ras" type = "boolean" checked = "true" label = "Using RAS datasets." />
106
107 <when value = "true">
108 <repeat name="input_datasets" title="RAS dataset" min="2">
109 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
110 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
111 </repeat>
112 </when>
113 </conditional>
114
115 <conditional name = "using_rps">
116 <param name = "check" argument = "--using_rps" type = "boolean" checked = "false" label = "Using RPS datasets." />
117
118 <when value = "true">
119 <repeat name="input_datasets_rps" title="RPS dataset" min="2">
120 <param name="input_rps" argument="--input_datas_rps" type="data" format="tabular, csv, tsv" label="add dataset" />
121 <param name="input_name_rps" argument="--names_rps" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
122 </repeat>
123 </when>
124 </conditional>
125 </when>
126
127 <when value="dataset_class">
128 <conditional name = "using_ras_all">
129 <param name = "check" argument = "--using_ras_all" type = "boolean" checked = "true" label = "Using RAS datasets." />
130
131 <when value = "true">
132 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" />
133 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
134 </when>
135 </conditional>
136
137 <conditional name = "using_rps_all">
138 <param name = "check" argument = "--using_rps_all" type = "boolean" checked = "false" label = "Using RPS datasets." />
139
140 <when value = "true">
141 <param name="input_data_rps" argument="--input_data_rps" type="data" format="tabular, csv, tsv" label="RPS of all samples" />
142 <param name="input_class_rps" argument="--input_class_rps" type="data" format="tabular, csv, tsv" label="Sample group specification" />
143 </when>
144 </conditional>
145 </when>
146 </conditional>
147
148 <conditional name="comparis">
149 <param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
150 <option value="manyvsmany" selected="true">One vs One</option>
151 <option value="onevsrest">One vs All</option>
152 <option value="onevsmany">One vs Control</option>
153 </param>
154 <when value="onevsmany">
155 <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
156 </when>
157 </conditional>
158
159 <conditional name="cond_choice_map">
160 <param name="choice_map" argument="--choice_map" type="select" label="Choose metabolic map:">
161 <option value="HMRcore" selected="true">HMRcore</option>
162 <option value="ENGRO2">ENGRO2</option>
163 <option value="Custom">Custom</option>
164 </param>
165
166 <when value="Custom">
167 <param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
168 </when>
169 </conditional>
170
171 <conditional name="advanced">
172 <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.">
173 <option value="true" selected="true">No</option>
174 <option value="false">Yes</option>
175 </param>
176
177 <when value="true">
178 <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold:" help="min value 0" />
179 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
180 <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?" />
181 <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?" />
182
183 <param name="netRPS" argument="--net" type="boolean" checked="false" label="Should RPS enrichment use net values?" help="If checked and RPS datasets are present the arrow tips of a reversible arrow will be colored with the net contribution of both directions' RPS values" />
184 </when>
185 </conditional>
186 </inputs>
187
188 <outputs>
189 <data format="txt" name="log" label="MaREA - Log" />
190 <collection name="results" type="list" label="MaREA - Results">
191 <discover_datasets pattern="__name_and_ext__" directory="result"/>
192 </collection>
193 </outputs>
194
195 <help>
196 <![CDATA[
197
198 What it does
199 -------------
200
201 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.
202
203 Accepted files are:
204 - 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");
205 - option 2) one RAS dataset and one group-file specifying the group each sample belongs to.
206
207 RAS datasets format: tab-separated text files, reporting the RAS value of each reaction (row) for a given sample (column).
208
209 Column header: sample ID.
210 Row header: reaction ID.
211
212 Optional files:
213 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
214
215 The tool generates:
216 - 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
217 - 2) a metabolic map file (downloadable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
218 - 3) a log file (.txt).
219
220 Output options:
221 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’).
222
223 Alternative options are:
224 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
225 - 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.
226
227 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".
228
229 Example input
230 -------------
231
232 "RAS of group 1 + RAS of group 2 + ... + RAS of group N" option:
233
234 RAS Dataset 1:
235
236 +------------+----------------+----------------+----------------+
237 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
238 +============+================+================+================+
239 | r1642 | 0.523167 | 0.371355 | 0.925661 |
240 +------------+----------------+----------------+----------------+
241 | r1643 | 0.568765 | 0.765567 | 0.456789 |
242 +------------+----------------+----------------+----------------+
243 | r1640 | 0.876545 | 0.768933 | 0.987654 |
244 +------------+----------------+----------------+----------------+
245 | r1641 | 0.456788 | 0.876543 | 0.876542 |
246 +------------+----------------+----------------+----------------+
247 | r1646 | 0.876543 | 0.786543 | 0.897654 |
248 +------------+----------------+----------------+----------------+
249
250 RAS Dataset 2:
251
252 +------------+----------------+----------------+----------------+
253 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
254 +============+================+================+================+
255 | r1642 | 0.523167 | 0.371355 | 0.925661 |
256 +------------+----------------+----------------+----------------+
257 | r1643 | 0.568765 | 0.765567 | 0.456789 |
258 +------------+----------------+----------------+----------------+
259 | r1640 | 0.876545 | 0.768933 | 0.987654 |
260 +------------+----------------+----------------+----------------+
261 | r1641 | 0.456788 | 0.876543 | 0.876542 |
262 +------------+----------------+----------------+----------------+
263 | r1646 | 0.876543 | 0.786543 | 0.897654 |
264 +------------+----------------+----------------+----------------+
265
266 "RAS of all samples + sample group specification" option:
267
268 RAS Dataset:
269
270 +------------+----------------+----------------+----------------+
271 | Reaction ID| TCGAA62670 | TCGAA62671 | TCGAA62672 |
272 +============+================+================+================+
273 | r1642 | 0.523167 | 0.371355 | 0.925661 |
274 +------------+----------------+----------------+----------------+
275 | r1643 | 0.568765 | 0.765567 | 0.456789 |
276 +------------+----------------+----------------+----------------+
277 | r1640 | 0.876545 | 0.768933 | 0.987654 |
278 +------------+----------------+----------------+----------------+
279 | r1641 | 0.456788 | 0.876543 | 0.876542 |
280 +------------+----------------+----------------+----------------+
281 | r1646 | 0.876543 | 0.786543 | 0.897654 |
282 +------------+----------------+----------------+----------------+
283
284 Group-file
285
286 +---------------+-----------+
287 | Patient ID | Class |
288 +===============+===========+
289 | TCGAAA3529 | MSI |
290 +---------------+-----------+
291 | TCGAA62671 | MSS |
292 +---------------+-----------+
293 | TCGAA62672 | MSI |
294 +---------------+-----------+
295
296 Advanced options
297 ----------------
298
299 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
300
301 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;
302
303
304 .. class:: infomark
305
306 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
307
308 .. class:: infomark
309
310 **TIP**: If your dataset is not split into classes, use MaREA cluster analysis.
311
312 .. class:: infomark
313
314 **TIP**: This tool using the RAS scores computed by Ras generator tool.
315
316 @REFERENCE@
317
318 .. _Ras tool: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA+RAS+Generator%2F1.0.6&version=1.0.6&__identifer=auulv6gbp76
319 .. _Convert delimiters to TAB: http://bimib.disco.unimib.it:5555/?tool_id=Convert+characters1&version=1.0.0&__identifer=76g7trea4j6
320 .. _MaREA cluster analysis: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA_cluester%2F1.1.2&version=1.1.2&__identifer=lxbyzn2me9
321
322 ]]>
323 </help>
324 <expand macro="citations" />
325 </tool>