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date Tue, 15 Oct 2019 12:21:16 -0400
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1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.3">
2 <description></description>
3 <macros>
4 <import>marea_macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="0.23.0">pandas</requirement>
8 <requirement type="package" version="1.1.0">scipy</requirement>
9 <requirement type="package" version="0.10.1">cobra</requirement>
10 <requirement type="package" version="4.2.1">lxml</requirement>
11 <requirement type="package" version="0.8.1">svglib</requirement>
12 <requirement type="package" version="3.4.0">reportlab</requirement>
13 </requirements>
14 <command detect_errors="exit_code">
15 <![CDATA[
16 python $__tool_directory__/marea.py
17 --rules_selector $cond_rule.rules_selector
18 #if $cond_rule.rules_selector == 'Custom':
19 --custom ${cond_rule.Custom_rules}
20 --yes_no ${cond_rule.cond_map.yes_no}
21 #if $cond_rule.cond_map.yes_no == 'yes':
22 --custom_map $cond_rule.cond_map.Custom_map
23 #end if
24 #end if
25
26 --tool_dir $__tool_directory__
27 --option $cond.type_selector
28 --out_log $log
29
30 #if $cond.type_selector == 'datasets':
31 --input_datas
32 #for $data in $cond.input_Datasets:
33 ${data.input}
34 #end for
35 --names
36 #for $data in $cond.input_Datasets:
37 ${data.input_name}
38 #end for
39 #if $cond.advanced.choice == 'true':
40 --none ${cond.advanced.None}
41 --pValue ${cond.advanced.pValue}
42 --fChange ${cond.advanced.fChange}
43 --generate_svg ${cond.advanced.generateSvg}
44 --generate_pdf ${cond.advanced.generatePdf}
45 --generate_ras ${cond.advanced.generateRas}
46 #else
47 --none true
48 --pValue 0.05
49 --fChange 1.5
50 --generate_svg false
51 --generate_pdf true
52 --generate_ras false
53 #end if
54 #elif $cond.type_selector == 'dataset_class':
55 --input_data ${input_data}
56 --input_class ${input_class}
57 #if $cond.advanced.choice == 'true':
58 --none ${cond.advanced.None}
59 --pValue ${cond.advanced.pValue}
60 --fChange ${cond.advanced.fChange}
61 --generate_svg ${cond.advanced.generateSvg}
62 --generate_pdf ${cond.advanced.generatePdf}
63 --generate_ras ${cond.advanced.generateRas}
64 #else
65 --none true
66 --pValue 0.05
67 --fChange 1.5
68 --generate_svg false
69 --generate_pdf true
70 --generate_ras false
71 #end if
72 #end if
73 #if $cond.type_selector == 'datasets_rasonly':
74 --input_datas ${input_Datasets}
75 --single_ras_file $ras_single
76 --none ${cond.advanced.None}
77 #end if
78 ]]>
79 </command>
80
81 <inputs>
82 <conditional name="cond_rule">
83 <expand macro="options"/>
84 <when value="HMRcore">
85 </when>
86 <when value="Recon">
87 </when>
88 <when value="Custom">
89 <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
90 <conditional name="cond_map">
91 <param name="yes_no" type="select" label="Custom map? (optional)">
92 <option value="no" selected="true">no</option>
93 <option value="yes">yes</option>
94 </param>
95 <when value="yes">
96 <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
97 </when>
98 <when value="no">
99 </when>
100 </conditional>
101 </when>
102 </conditional>
103 <conditional name="cond">
104 <param name="type_selector" argument="--option" type="select" label="Input format:">
105 <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
106 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
107 <option value="datasets_rasonly" selected="true">RNAseq dataset</option>
108 </param>
109 <when value="datasets">
110 <repeat name="input_Datasets" title="RNAseq" min="2">
111 <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
112 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
113 </repeat>
114 <conditional name="advanced">
115 <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
116 <option value="true" selected="true">No</option>
117 <option value="false">Yes</option>
118 </param>
119 <when value="false">
120 </when>
121 <when value="true">
122 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
123 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
124 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
125 <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?" />
126 <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?" />
127 <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" />
128 </when>
129 </conditional>
130 </when>
131 <when value="datasets_rasonly">
132 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />
133 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
134 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
135 </when>
136 <when value="dataset_class">
137 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
138 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
139 <conditional name="advanced">
140 <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom rules for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
141 <option value="true" selected="true">No</option>
142 <option value="false">Yes</option>
143 </param>
144 <when value="false">
145 </when>
146 <when value="true">
147 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
148 <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" />
149 <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
150 <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?" />
151 <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?" />
152 <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" />
153 </when>
154 </conditional>
155 </when>
156 </conditional>
157
158
159
160
161 </inputs>
162
163 <outputs>
164 <data format="txt" name="log" label="MaREA - Log" />
165 <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
166 <filter>cond['type_selector'] == "datasets_rasonly"</filter>
167 </data>
168 <collection name="results" type="list" label="MaREA - Results">
169 <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
170 <discover_datasets pattern="__name_and_ext__" directory="result"/>
171 </collection>
172 <collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
173 <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
174 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
175 </collection>
176
177 </outputs>
178 <tests>
179 <test>
180 <param name="pValue" value="0.56"/>
181 <output name="log" file="log.txt"/>
182 </test>
183 </tests>
184 <help>
185 <![CDATA[
186
187 What it does
188 -------------
189
190 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.
191
192 Accepted files are:
193 - 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*");
194 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
195
196 Optional files:
197 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
198
199 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
200 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
201 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
202
203 The tool generates:
204 1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
205 2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
206 3) a log file (.txt).
207
208 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.
209
210 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).
211
212 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
213
214 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".
215
216
217 Example input
218 -------------
219
220 **"Custom Rules"** option:
221
222 Custom Rules Dastaset:
223
224 @CUSTOM_RULES_EXEMPLE@
225
226 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
227
228 RNA-seq Dataset 1:
229
230 @DATASET_EXEMPLE1@
231
232 RNA-seq Dataset 2:
233
234 @DATASET_EXEMPLE2@
235
236 **"RNAseq of all samples + sample group specification"** option:
237
238 RNA-seq Dataset:
239
240 @DATASET_EXEMPLE1@
241
242 Class-file:
243
244 +------------+------------+
245 | Patient_ID | class |
246 +============+============+
247 | TCGAAA3529 | MSI |
248 +------------+------------+
249 | TCGAA62671 | MSS |
250 +------------+------------+
251 | TCGAA62672 | MSI |
252 +------------+------------+
253
254 |
255
256 .. class:: infomark
257
258 **TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
259
260 .. class:: infomark
261
262 **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
263
264 @REFERENCE@
265
266 .. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
267 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
268 .. _MaREA cluster analysis: http://link del tool di cluster.org
269
270 ]]>
271 </help>
272 <expand macro="citations" />
273 </tool>
274