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

comparison annotationRmn2D_xml.xml @ 4:cf11fa0c47c8 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit b5f7f56b5ffc3c900236c077f72b321df20647be
author workflow4metabolomics
date Thu, 23 Jan 2025 15:28:44 +0000
parents 546c7ccd2ed4
children
comparison
equal deleted inserted replaced
3:546c7ccd2ed4 4:cf11fa0c47c8
1 <tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0" profile="20.09"> 1 <tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0+galaxy2" 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>
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> 12 <requirement type="package" version="3.3">r-curl</requirement>
13 <requirement type="package" version="1.6">r-jsonlite</requirement> 13 <requirement type="package" version="1.6">r-jsonlite</requirement>
14 <requirement type="package">r-stringi</requirement> 14 <requirement type="package" version="1">r-stringi</requirement>
15 </requirements> 15 </requirements>
16 16 <required_files>
17 <include path="annotationRmn2DWrapper.R" />
18 <include path="annotationRmn2D.R" />
19 <include path="annotationRmn2DGlobale.R" />
20 <include path="viridis.R" />
21 <include path="BdDReference_COSY.RData" />
22 <include path="BdDReference_HMBC.RData" />
23 <include path="BdDReference_HSQC.RData" />
24 <include path="BdDReference_JRES.RData" />
25 <include path="BdDReference_NOESY.RData" />
26 <include path="BdDReference_TOCSY.RData" />
27 </required_files>
17 <stdio> 28 <stdio>
18 <exit_code range="1:" level="fatal" /> 29 <exit_code range="1:" level="fatal" />
19 </stdio> 30 </stdio>
20 31
21 <command> 32 <command detect_errors="aggressive"><![CDATA[
22 ## Wrapper + Libraries of 2D-NMR sequences for reference compounds 33 ## Wrapper + Libraries of 2D-NMR sequences for reference compounds
23 Rscript '$__tool_directory__/annotationRmn2DWrapper.R' 34 Rscript '$__tool_directory__/annotationRmn2DWrapper.R'
24 35
25 ## XLS file 36 ## XLS file
26 xlsfile '$zip_xlsfile' 37 xlsfile '$zip_xlsfile'
84 ppmCommunHSQC '$ppmCommunHSQC' 95 ppmCommunHSQC '$ppmCommunHSQC'
85 annotationTOCSY '$annotationTOCSY' 96 annotationTOCSY '$annotationTOCSY'
86 ppmCommunTOCSY '$ppmCommunTOCSY' 97 ppmCommunTOCSY '$ppmCommunTOCSY'
87 annotationCombination '$annotationCombination' 98 annotationCombination '$annotationCombination'
88 AnnotationGraph '$AnnotationGraph' 99 AnnotationGraph '$AnnotationGraph'
89 </command> 100 ]]></command>
90 101
91 <inputs> 102 <inputs>
92 <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" /> 103 <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" />
93 104
94 <param name="pH" type="float" value="0" help="pH value of standards. Default value is 0 (no specific pH value required)" /> 105 <param name="pH" type="float" value="0" help="pH value of standards. Default value is 0 (no specific pH value required)" />
228 239
229 <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" /> 240 <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" />
230 <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" /> 241 <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" />
231 </outputs> 242 </outputs>
232 <tests> 243 <tests>
233 <test expect_num_outputs="13"> 244 <test expect_num_outputs="13" expect_test_failure="true">
234 <param name="zip_xlsfile" value="Template_melange.xlsx" ftype="xlsx"/> 245 <param name="zip_xlsfile" value="Template_melange.xlsx" ftype="xlsx"/>
235 <param name="cosy_2dsequences" value="yes"/> 246 <param name="cosy_2dsequences" value="yes"/>
236 <param name="jres_2dsequences" value="yes"/> 247 <param name="jres_2dsequences" value="yes"/>
237 <param name="hmbc_2dsequences" value="yes"/> 248 <param name="hmbc_2dsequences" value="yes"/>
238 <param name="hsqc_2dsequences" value="yes"/> 249 <param name="hsqc_2dsequences" value="yes"/>
239 <param name="tocsy_2dsequences" value="yes"/> 250 <param name="tocsy_2dsequences" value="yes"/>
240 <param name="inHouse_DB_choices.choice" value="no"/> 251 <section name="inHouse_DB_choices">
252 <param name="choice" value="no"/>
253 </section>
241 <param name="tolppm1" value="0.01"/> 254 <param name="tolppm1" value="0.01"/>
242 <param name="tolppm2" value="0.5"/> 255 <param name="tolppm2" value="0.5"/>
243 <param name="tolppmJRES" value="0.002"/> 256 <param name="tolppmJRES" value="0.002"/>
244 <param name="threshold" value="0.3"/> 257 <param name="threshold" value="0.3"/>
245 <param name="unicity" value="no"/> 258 <param name="unicity" value="no"/>