Mercurial > repos > marie-tremblay-metatoul > 2dnmrannotation

comparison annotationRmn2D_xml.xml @ 3:546c7ccd2ed4 draft default tip

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"planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 911f4beba3dcb25c1033e8239426f8f763683523"
author workflow4metabolomics
date Fri, 04 Feb 2022 09:01:11 +0000
parents dff7bde22102
children
comparison
equal deleted inserted replaced
2:dff7bde22102 3:546c7ccd2ed4
1 <tool id="2DNmrAnnotation" name="2DNMR_Annotation" version="1.0.0"> 1 <tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0" profile="20.09">
2 2
3 <description> Annotation of complex mixture bidimensional NMR spectra </description> 3 <description> Annotation of complex mixture bidimensional NMR spectra </description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" version="1.1_5">r-batch</requirement> 6 <requirement type="package" version="1.1_5">r-batch</requirement>
7 <requirement type="package" version="0.8.3">r-dplyr</requirement> 7 <requirement type="package" version="0.8.3">r-dplyr</requirement>
8 <requirement type="package" version="3.2.1">r-ggplot2</requirement> 8 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
9 <requirement type="package" version="4.0.17">r-openxlsx</requirement> 9 <requirement type="package" version="4.0.17">r-openxlsx</requirement>
10 <requirement type="package" version="1.4.0">r-stringr</requirement> 10 <requirement type="package" version="1.4.0">r-stringr</requirement>
11 <requirement type="package" version="1.0.2">r-tidyr</requirement> 11 <requirement type="package" version="1.0.2">r-tidyr</requirement>
12 <requirement type="package" version="3.3">r-curl</requirement>
13 <requirement type="package" version="1.6">r-jsonlite</requirement>
14 <requirement type="package">r-stringi</requirement>
12 </requirements> 15 </requirements>
13 16
14 <stdio> 17 <stdio>
15 <exit_code range="1:" level="fatal" /> 18 <exit_code range="1:" level="fatal" />
16 </stdio> 19 </stdio>
17 20
18 <command> 21 <command>
19 ## Wrapper + Libraries of 2D-NMR sequences for reference compounds 22 ## Wrapper + Libraries of 2D-NMR sequences for reference compounds
20 Rscript '$__tool_directory__/annotationRmn2DWrapper.R' 23 Rscript '$__tool_directory__/annotationRmn2DWrapper.R'
21 24
22
23 ## XLS file 25 ## XLS file
24 xlsfile '$zip_xlsfile' 26 xlsfile '$zip_xlsfile'
27
28 ## Parameters to reduce search
29 pH $pH
30 magneticField $magneticField
25 31
26 ## 2D-NMR sequences to annotate 32 ## 2D-NMR sequences to annotate
27 cosy_2dsequences $cosy_2dsequences 33 cosy_2dsequences $cosy_2dsequences
28 jres_2dsequences $jres_2dsequences 34 jres_2dsequences $jres_2dsequences
29 hmbc_2dsequences $hmbc_2dsequences 35 hmbc_2dsequences $hmbc_2dsequences
58 ## Tolerances 64 ## Tolerances
59 tolppm1 $tolppm1 65 tolppm1 $tolppm1
60 tolppm2 $tolppm2 66 tolppm2 $tolppm2
61 tolppmJRES $tolppmJRES 67 tolppmJRES $tolppmJRES
62 68
63
64 ## Treshold (probability score) 69 ## Treshold (probability score)
65 threshold $threshold 70 threshold $threshold
66 71
67 ## Unicity 72 ## Unicity
68 unicity $unicity 73 unicity $unicity
79 ppmCommunHSQC '$ppmCommunHSQC' 84 ppmCommunHSQC '$ppmCommunHSQC'
80 annotationTOCSY '$annotationTOCSY' 85 annotationTOCSY '$annotationTOCSY'
81 ppmCommunTOCSY '$ppmCommunTOCSY' 86 ppmCommunTOCSY '$ppmCommunTOCSY'
82 annotationCombination '$annotationCombination' 87 annotationCombination '$annotationCombination'
83 AnnotationGraph '$AnnotationGraph' 88 AnnotationGraph '$AnnotationGraph'
84
85 </command> 89 </command>
86 90
87 <inputs> 91 <inputs>
88 <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" /> 92 <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" />
93
94 <param name="pH" type="float" value="0" help="pH value of standards. Default value is 0 (no specific pH value required)" />
95 <param name="magneticField" type="integer" value="0" help="Magnetic filed of NMR spectrometer used to generate standard spectra. Default value is 0 (no specific field required)" />
89 96
90 <param name="cosy_2dsequences" type="select" label="2D-NMR COSY sequence"> 97 <param name="cosy_2dsequences" type="select" label="2D-NMR COSY sequence">
91 <option value="yes" > yes </option> 98 <option value="yes" > yes </option>
92 <option value="no" selected="true"> no </option> 99 <option value="no" selected="true"> no </option>
93 </param> 100 </param>
94 <param name="jres_2dsequences" type="select" label="2D-NMR JRES sequence">
95 <option value="yes" > yes </option>
96 <option value="no" selected="true"> no </option>
97 </param>
98 <param name="hmbc_2dsequences" type="select" label="2D-NMR HMBC sequence"> 101 <param name="hmbc_2dsequences" type="select" label="2D-NMR HMBC sequence">
99 <option value="yes" > yes </option> 102 <option value="yes" > yes </option>
100 <option value="no" selected="true"> no </option> 103 <option value="no" selected="true"> no </option>
101 </param> 104 </param>
102 <param name="hsqc_2dsequences" type="select" label="2D-NMR HSQC sequence"> 105 <param name="hsqc_2dsequences" type="select" label="2D-NMR HSQC sequence">
106 <option value="yes" > yes </option>
107 <option value="no" selected="true"> no </option>
108 </param>
109 <param name="jres_2dsequences" type="select" label="2D-NMR JRES sequence">
103 <option value="yes" > yes </option> 110 <option value="yes" > yes </option>
104 <option value="no" selected="true"> no </option> 111 <option value="no" selected="true"> no </option>
105 </param> 112 </param>
106 <param name="tocsy_2dsequences" type="select" label="2D-NMR TOCSY sequence"> 113 <param name="tocsy_2dsequences" type="select" label="2D-NMR TOCSY sequence">
107 <option value="yes" > yes </option> 114 <option value="yes" > yes </option>
166 </conditional> 173 </conditional>
167 </when> 174 </when>
168 <when value="no" /> 175 <when value="no" />
169 </conditional> 176 </conditional>
170 177
171 <param name="tolppm1" type="float" value="0.01" help="Tolerance on chemical shift for the x-axis (H). Default value is 0.01ppm" /> 178 <param name="tolppm1" type="float" min="0" value="0.01" help="Tolerance on chemical shift for the x-axis (H). Default value is 0.01ppm" />
172 <param name="tolppm2" type="float" value="0.5" help="Tolerance on chemical shift for the y-axis (C). Default value is 0.01ppm" /> 179 <param name="tolppm2" type="float" min="0" value="0.5" help="Tolerance on chemical shift for the y-axis (C). Default value is 0.01ppm" />
173 <param name="tolppmJRES" type="float" value="0.002" help="Tolerance on chemical shift for the y-axis for the JRES sequence. Default value is 0.002 (Hz)" /> 180 <param name="tolppmJRES" type="float" min="0" value="0.002" help="Tolerance on chemical shift for the y-axis for the JRES sequence. Default value is 0.002 (Hz)" />
174 181
175 <param name="threshold" type="float" value="0" help="Treshold on score of presence. Default value is 0" /> 182 <param name="threshold" type="float" min="0" max="1" value="0" help="Treshold on score of presence. Default value is 0" />
176 183
177 <param name="unicity" label="Unicity of annotation" type="select" display="radio" help=""> 184 <param name="unicity" label="Unicity of annotation" type="select" display="radio" help="Select only chemical shifts corresponding to one one metabolite">
178 <option value="no">No</option> 185 <option value="no">No</option>
179 <option value="yes"></option> 186 <option value="yes">Yes</option>
180 </param> 187 </param>
181 188
182 </inputs> 189 </inputs>
183 190
184 <outputs> 191 <outputs>
185 <data format="txt" name="logOut" label="${tool.name}_log" /> 192 <data format="txt" name="logOut" label="${tool.name}_log" />
186 <data format="tabular" name="annotationCOSY" label="annotationCosy" > 193
194 <data format="tabular" name="annotationCOSY" label="${tool.name}_annotationCOSY" >
187 <filter> cosy_2dsequences != "no" </filter> 195 <filter> cosy_2dsequences != "no" </filter>
188 </data> 196 </data>
189 <data format="tabular" name="ppmCommunCOSY" label="duplicateCosy" > 197 <data format="tabular" name="ppmCommunCOSY" label="${tool.name}_uplicateCOSY" >
190 <filter> cosy_2dsequences != "no" </filter> 198 <filter> cosy_2dsequences != "no" </filter>
191 </data> 199 </data>
192 200
193 <data format="tabular" name="annotationJRES" label="annotationJres" > 201 <data format="tabular" name="annotationJRES" label="${tool.name}_annotationJRES" >
194 <filter> jres_2dsequences != "no" </filter> 202 <filter> jres_2dsequences != "no" </filter>
195 </data> 203 </data>
196 <data format="tabular" name="ppmCommunJRES" label="duplicateJres" > 204 <data format="tabular" name="ppmCommunJRES" label="${tool.name}_duplicateJRES" >
197 <filter> jres_2dsequences != "no" </filter> 205 <filter> jres_2dsequences != "no" </filter>
198 </data> 206 </data>
199 207
200 <data format="tabular" name="annotationHMBC" label="annotationHmbc" > 208 <data format="tabular" name="annotationHMBC" label="${tool.name}_annotationHMBC" >
201 <filter> hmbc_2dsequences != "no" </filter> 209 <filter> hmbc_2dsequences != "no" </filter>
202 </data> 210 </data>
203 <data format="tabular" name="ppmCommunHMBC" label="duplicateHmbc" > 211 <data format="tabular" name="ppmCommunHMBC" label="${tool.name}_duplicateHMBC" >
204 <filter> hmbc_2dsequences != "no" </filter> 212 <filter> hmbc_2dsequences != "no" </filter>
205 </data> 213 </data>
206 214
207 <data format="tabular" name="annotationHSQC" label="annotationHsqc" > 215 <data format="tabular" name="annotationHSQC" label="${tool.name}_annotationHSQC" >
208 <filter> hsqc_2dsequences != "no" </filter> 216 <filter> hsqc_2dsequences != "no" </filter>
209 </data> 217 </data>
210 <data format="tabular" name="ppmCommunHSQC" label="duplicateHsqc" > 218 <data format="tabular" name="ppmCommunHSQC" label="${tool.name}_duplicateHSQC" >
211 <filter> hsqc_2dsequences != "no" </filter> 219 <filter> hsqc_2dsequences != "no" </filter>
212 </data> 220 </data>
213 221
214 <data format="tabular" name="annotationTOCSY" label="annotationTocsy" > 222 <data format="tabular" name="annotationTOCSY" label="${tool.name}_annotationTOCSY" >
215 <filter> tocsy_2dsequences != "no" </filter> 223 <filter> tocsy_2dsequences != "no" </filter>
216 </data> 224 </data>
217 <data format="tabular" name="ppmCommunTOCSY" label="duplicateTocsy" > 225 <data format="tabular" name="ppmCommunTOCSY" label="${tool.name}_duplicateTOCSY" >
218 <filter> tocsy_2dsequences != "no" </filter> 226 <filter> tocsy_2dsequences != "no" </filter>
219 </data> 227 </data>
220 228
221 <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" /> 229 <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" />
222 <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" /> 230 <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" />
223 </outputs> 231 </outputs>
224 <tests> 232 <tests>
225 <test> 233 <test expect_num_outputs="13">
226 <param name="zip_xlsfile" value="Template_melange.xlsm" ftype="xlsx"/> 234 <param name="zip_xlsfile" value="Template_melange.xlsx" ftype="xlsx"/>
227 <param name="cosy_2dsequences" value="no"/> 235 <param name="cosy_2dsequences" value="yes"/>
228 <param name="jres_2dsequences" value="yes"/> 236 <param name="jres_2dsequences" value="yes"/>
229 <param name="hmbc_2dsequences" value="no"/> 237 <param name="hmbc_2dsequences" value="yes"/>
230 <param name="hsqc_2dsequences" value="yes"/> 238 <param name="hsqc_2dsequences" value="yes"/>
231 <param name="tocsy_2dsequences" value="no"/> 239 <param name="tocsy_2dsequences" value="yes"/>
232 <param name="tocsy_2dsequences" value="no"/> 240 <param name="inHouse_DB_choices.choice" value="no"/>
233 <param name="inHouse_DB_choices.choice" value="no"/> 241 <param name="tolppm1" value="0.01"/>
234 <param name="tolppm1" value="0.01"/> 242 <param name="tolppm2" value="0.5"/>
235 <param name="tolppm2" value="0.5"/> 243 <param name="tolppmJRES" value="0.002"/>
236 <param name="tolppmJRES" value="0.002"/> 244 <param name="threshold" value="0.3"/>
237 <param name="threshold" value="0.3"/> 245 <param name="unicity" value="no"/>
238 <param name="unicity" value="no"/> 246 <output name="annotationCOSY" file="2DNMRAnnotation_annotationCOSY.tabular"/>
239 <output name="annotationJRES" file="annotationJres.tabular"/> 247 <output name="ppmCommunCOSY" file="2DNMRAnnotation_duplicateCOSY.tabular"/>
240 <output name="ppmCommunJRES" file="duplicateJres.tabular"/> 248 <output name="annotationHMBC" file="2DNMRAnnotation_annotationHMBC.tabular"/>
241 <output name="annotationHSQC" file="annotationHsqc.tabular"/> 249 <output name="ppmCommunHMBC" file="2DNMRAnnotation_duplicateHMBC.tabular"/>
242 <output name="ppmCommunHSQC" file="duplicateHsqc.tabular"/> 250 <output name="annotationHSQC" file="2DNMRAnnotation_annotationHSQC.tabular"/>
243 <output name="annotationCombination" file="2DNMR_Annotation_annotationCombination.tabular"/> 251 <output name="ppmCommunHSQC" file="2DNMRAnnotation_duplicateHSQC.tabular"/>
244 </test> 252 <output name="annotationJRES" file="2DNMRAnnotation_annotationJRES.tabular"/>
245 </tests> 253 <output name="ppmCommunJRES" file="2DNMRAnnotation_duplicateJRES.tabular"/>
246 <help> 254 <output name="annotationTOCSY" file="2DNMRAnnotation_annotationTOCSY.tabular"/>
255 <output name="ppmCommunTOCSY" file="2DNMRAnnotation_duplicateTOCSY.tabular"/>
256 <output name="annotationCombination" file="2DNMRAnnotation_annotationCombination.tabular"/>
257 </test>
258 </tests>
259 <help>
247 260
248 .. class:: infomark 261 .. class:: infomark
249 262
250 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Coline Gardou 263 **Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Coline Gardou
251 264