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comparison Marea/marea.xml @ 32:b795e3e163e0 draft

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bug fix
author bimib
date Wed, 16 Oct 2019 07:12:37 -0400
parents 944e15aa970a
children abf0bfe01c78
comparison
equal deleted inserted replaced
31:944e15aa970a 32:b795e3e163e0
1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.3"> 1 <tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.4">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>marea_macros.xml</import> 4 <import>marea_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
20 --yes_no ${cond_rule.cond_map.yes_no} 20 --yes_no ${cond_rule.cond_map.yes_no}
21 #if $cond_rule.cond_map.yes_no == 'yes': 21 #if $cond_rule.cond_map.yes_no == 'yes':
22 --custom_map $cond_rule.cond_map.Custom_map 22 --custom_map $cond_rule.cond_map.Custom_map
23 #end if 23 #end if
24 #end if 24 #end if
25 25
26 --tool_dir $__tool_directory__ 26 --tool_dir $__tool_directory__
27 --option $cond.type_selector 27 --option $cond.type_selector
28 --out_log $log 28 --out_log $log
29 29
30 #if $cond.type_selector == 'datasets': 30 #if $cond.type_selector == 'datasets':
31 --input_datas 31 --input_datas
32 #for $data in $cond.input_Datasets: 32 #for $data in $cond.input_Datasets:
33 ${data.input} 33 ${data.input}
34 #end for 34 #end for
41 --pValue ${cond.advanced.pValue} 41 --pValue ${cond.advanced.pValue}
42 --fChange ${cond.advanced.fChange} 42 --fChange ${cond.advanced.fChange}
43 --generate_svg ${cond.advanced.generateSvg} 43 --generate_svg ${cond.advanced.generateSvg}
44 --generate_pdf ${cond.advanced.generatePdf} 44 --generate_pdf ${cond.advanced.generatePdf}
45 --generate_ras ${cond.advanced.generateRas} 45 --generate_ras ${cond.advanced.generateRas}
46 #else 46 #else
47 --none true 47 --none true
48 --pValue 0.05 48 --pValue 0.05
49 --fChange 1.5 49 --fChange 1.5
50 --generate_svg false 50 --generate_svg false
51 --generate_pdf true 51 --generate_pdf true
59 --pValue ${cond.advanced.pValue} 59 --pValue ${cond.advanced.pValue}
60 --fChange ${cond.advanced.fChange} 60 --fChange ${cond.advanced.fChange}
61 --generate_svg ${cond.advanced.generateSvg} 61 --generate_svg ${cond.advanced.generateSvg}
62 --generate_pdf ${cond.advanced.generatePdf} 62 --generate_pdf ${cond.advanced.generatePdf}
63 --generate_ras ${cond.advanced.generateRas} 63 --generate_ras ${cond.advanced.generateRas}
64 #else 64 #else
65 --none true 65 --none true
66 --pValue 0.05 66 --pValue 0.05
67 --fChange 1.5 67 --fChange 1.5
68 --generate_svg false 68 --generate_svg false
69 --generate_pdf true 69 --generate_pdf true
71 #end if 71 #end if
72 #end if 72 #end if
73 #if $cond.type_selector == 'datasets_rasonly': 73 #if $cond.type_selector == 'datasets_rasonly':
74 --input_datas ${input_Datasets} 74 --input_datas ${input_Datasets}
75 --single_ras_file $ras_single 75 --single_ras_file $ras_single
76 --none ${cond.advanced.None} 76 --none ${None}
77 #end if 77 #end if
78 ]]> 78 ]]>
79 </command> 79 </command>
80 80
81 <inputs> 81 <inputs>
106 <option value="dataset_class">RNAseq of all samples + sample group specification</option> 106 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
107 <option value="datasets_rasonly" selected="true">RNAseq dataset</option> 107 <option value="datasets_rasonly" selected="true">RNAseq dataset</option>
108 </param> 108 </param>
109 <when value="datasets"> 109 <when value="datasets">
110 <repeat name="input_Datasets" title="RNAseq" min="2"> 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" /> 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" /> 112 <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
113 </repeat> 113 </repeat>
114 <conditional name="advanced"> 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."> 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> 116 <option value="true" selected="true">No</option>
117 <option value="false">Yes</option> 117 <option value="false">Yes</option>
118 </param> 118 </param>
119 <when value="false"> 119 <when value="false">
120 </when> 120 </when>
121 <when value="true"> 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)?" /> 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" /> 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" /> 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?" /> 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?" /> 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" /> 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> 128 </when>
129 </conditional> 129 </conditional>
130 </when> 130 </when>
131 <when value="datasets_rasonly"> 131 <when value="datasets_rasonly">
132 <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> 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" /> 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)?" /> 134 <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
135 </when> 135 </when>
136 <when value="dataset_class"> 136 <when value="dataset_class">
137 <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> 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" /> 138 <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
139 <conditional name="advanced"> 139 <conditional name="advanced">
142 <option value="false">Yes</option> 142 <option value="false">Yes</option>
143 </param> 143 </param>
144 <when value="false"> 144 <when value="false">
145 </when> 145 </when>
146 <when value="true"> 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)?" /> 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" /> 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" /> 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?" /> 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?" /> 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" /> 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> 153 </when>
154 </conditional> 154 </conditional>
155 </when> 155 </when>
156 </conditional> 156 </conditional>
157 157
158 158
159 159
160 160
161 </inputs> 161 </inputs>
162 162
163 <outputs> 163 <outputs>
164 <data format="txt" name="log" label="MaREA - Log" /> 164 <data format="txt" name="log" label="MaREA - Log" />
165 <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}"> 165 <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
171 </collection> 171 </collection>
172 <collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular"> 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> 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"/> 174 <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
175 </collection> 175 </collection>
176 176
177 </outputs> 177 </outputs>
178 <tests> 178 <tests>
179 <test> 179 <test>
180 <param name="pValue" value="0.56"/> 180 <param name="pValue" value="0.56"/>
181 <output name="log" file="log.txt"/> 181 <output name="log" file="log.txt"/>
187 What it does 187 What it does
188 ------------- 188 -------------
189 189
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. 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.
191 191
192 Accepted files are: 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*"); 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. 194 - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
195 195
196 Optional files: 196 Optional files:
197 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats: 197 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
223 223
224 @CUSTOM_RULES_EXEMPLE@ 224 @CUSTOM_RULES_EXEMPLE@
225 225
226 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option: 226 **"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
227 227
228 RNA-seq Dataset 1: 228 RNA-seq Dataset 1:
229 229
230 @DATASET_EXEMPLE1@ 230 @DATASET_EXEMPLE1@
231 231
232 RNA-seq Dataset 2: 232 RNA-seq Dataset 2:
233 233
239 239
240 @DATASET_EXEMPLE1@ 240 @DATASET_EXEMPLE1@
241 241
242 Class-file: 242 Class-file:
243 243
244 +------------+------------+ 244 +------------+------------+
245 | Patient_ID | class | 245 | Patient_ID | class |
246 +============+============+ 246 +============+============+
247 | TCGAAA3529 | MSI | 247 | TCGAAA3529 | MSI |
248 +------------+------------+ 248 +------------+------------+
249 | TCGAA62671 | MSS | 249 | TCGAA62671 | MSS |
250 +------------+------------+ 250 +------------+------------+
251 | TCGAA62672 | MSI | 251 | TCGAA62672 | MSI |
252 +------------+------------+ 252 +------------+------------+
253 253
254 | 254 |
255 255
256 .. class:: infomark 256 .. class:: infomark
269 269
270 ]]> 270 ]]>
271 </help> 271 </help>
272 <expand macro="citations" /> 272 <expand macro="citations" />
273 </tool> 273 </tool>
274