Mercurial > repos > marie-tremblay-metatoul > 2dnmrannotation
diff annotationRmn2D_xml.xml @ 3:546c7ccd2ed4 draft default tip
"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 |
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--- a/annotationRmn2D_xml.xml Tue Feb 04 10:59:26 2020 -0500 +++ b/annotationRmn2D_xml.xml Fri Feb 04 09:01:11 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="2DNmrAnnotation" name="2DNMR_Annotation" version="1.0.0"> +<tool id="2DNmrAnnotation" name="2DNMRAnnotation" version="2.0.0" profile="20.09"> <description> Annotation of complex mixture bidimensional NMR spectra </description> @@ -9,6 +9,9 @@ <requirement type="package" version="4.0.17">r-openxlsx</requirement> <requirement type="package" version="1.4.0">r-stringr</requirement> <requirement type="package" version="1.0.2">r-tidyr</requirement> + <requirement type="package" version="3.3">r-curl</requirement> + <requirement type="package" version="1.6">r-jsonlite</requirement> + <requirement type="package">r-stringi</requirement> </requirements> <stdio> @@ -19,10 +22,13 @@ ## Wrapper + Libraries of 2D-NMR sequences for reference compounds Rscript '$__tool_directory__/annotationRmn2DWrapper.R' - ## XLS file xlsfile '$zip_xlsfile' + ## Parameters to reduce search + pH $pH + magneticField $magneticField + ## 2D-NMR sequences to annotate cosy_2dsequences $cosy_2dsequences jres_2dsequences $jres_2dsequences @@ -60,7 +66,6 @@ tolppm2 $tolppm2 tolppmJRES $tolppmJRES - ## Treshold (probability score) threshold $threshold @@ -81,20 +86,18 @@ ppmCommunTOCSY '$ppmCommunTOCSY' annotationCombination '$annotationCombination' AnnotationGraph '$AnnotationGraph' - </command> <inputs> <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" /> + <param name="pH" type="float" value="0" help="pH value of standards. Default value is 0 (no specific pH value required)" /> + <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)" /> + <param name="cosy_2dsequences" type="select" label="2D-NMR COSY sequence"> <option value="yes" > yes </option> <option value="no" selected="true"> no </option> </param> - <param name="jres_2dsequences" type="select" label="2D-NMR JRES sequence"> - <option value="yes" > yes </option> - <option value="no" selected="true"> no </option> - </param> <param name="hmbc_2dsequences" type="select" label="2D-NMR HMBC sequence"> <option value="yes" > yes </option> <option value="no" selected="true"> no </option> @@ -103,6 +106,10 @@ <option value="yes" > yes </option> <option value="no" selected="true"> no </option> </param> + <param name="jres_2dsequences" type="select" label="2D-NMR JRES sequence"> + <option value="yes" > yes </option> + <option value="no" selected="true"> no </option> + </param> <param name="tocsy_2dsequences" type="select" label="2D-NMR TOCSY sequence"> <option value="yes" > yes </option> <option value="no" selected="true"> no </option> @@ -168,53 +175,54 @@ <when value="no" /> </conditional> - <param name="tolppm1" type="float" value="0.01" help="Tolerance on chemical shift for the x-axis (H). Default value is 0.01ppm" /> - <param name="tolppm2" type="float" value="0.5" help="Tolerance on chemical shift for the y-axis (C). Default value is 0.01ppm" /> - <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)" /> + <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" /> + <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" /> + <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)" /> - <param name="threshold" type="float" value="0" help="Treshold on score of presence. Default value is 0" /> + <param name="threshold" type="float" min="0" max="1" value="0" help="Treshold on score of presence. Default value is 0" /> - <param name="unicity" label="Unicity of annotation" type="select" display="radio" help=""> + <param name="unicity" label="Unicity of annotation" type="select" display="radio" help="Select only chemical shifts corresponding to one one metabolite"> <option value="no">No</option> - <option value="yes"></option> + <option value="yes">Yes</option> </param> </inputs> <outputs> <data format="txt" name="logOut" label="${tool.name}_log" /> - <data format="tabular" name="annotationCOSY" label="annotationCosy" > + + <data format="tabular" name="annotationCOSY" label="${tool.name}_annotationCOSY" > <filter> cosy_2dsequences != "no" </filter> </data> - <data format="tabular" name="ppmCommunCOSY" label="duplicateCosy" > + <data format="tabular" name="ppmCommunCOSY" label="${tool.name}_uplicateCOSY" > <filter> cosy_2dsequences != "no" </filter> </data> - <data format="tabular" name="annotationJRES" label="annotationJres" > + <data format="tabular" name="annotationJRES" label="${tool.name}_annotationJRES" > <filter> jres_2dsequences != "no" </filter> </data> - <data format="tabular" name="ppmCommunJRES" label="duplicateJres" > + <data format="tabular" name="ppmCommunJRES" label="${tool.name}_duplicateJRES" > <filter> jres_2dsequences != "no" </filter> </data> - <data format="tabular" name="annotationHMBC" label="annotationHmbc" > + <data format="tabular" name="annotationHMBC" label="${tool.name}_annotationHMBC" > <filter> hmbc_2dsequences != "no" </filter> </data> - <data format="tabular" name="ppmCommunHMBC" label="duplicateHmbc" > + <data format="tabular" name="ppmCommunHMBC" label="${tool.name}_duplicateHMBC" > <filter> hmbc_2dsequences != "no" </filter> </data> - <data format="tabular" name="annotationHSQC" label="annotationHsqc" > + <data format="tabular" name="annotationHSQC" label="${tool.name}_annotationHSQC" > <filter> hsqc_2dsequences != "no" </filter> </data> - <data format="tabular" name="ppmCommunHSQC" label="duplicateHsqc" > + <data format="tabular" name="ppmCommunHSQC" label="${tool.name}_duplicateHSQC" > <filter> hsqc_2dsequences != "no" </filter> </data> - <data format="tabular" name="annotationTOCSY" label="annotationTocsy" > + <data format="tabular" name="annotationTOCSY" label="${tool.name}_annotationTOCSY" > <filter> tocsy_2dsequences != "no" </filter> </data> - <data format="tabular" name="ppmCommunTOCSY" label="duplicateTocsy" > + <data format="tabular" name="ppmCommunTOCSY" label="${tool.name}_duplicateTOCSY" > <filter> tocsy_2dsequences != "no" </filter> </data> @@ -222,28 +230,33 @@ <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" /> </outputs> <tests> - <test> - <param name="zip_xlsfile" value="Template_melange.xlsm" ftype="xlsx"/> - <param name="cosy_2dsequences" value="no"/> - <param name="jres_2dsequences" value="yes"/> - <param name="hmbc_2dsequences" value="no"/> - <param name="hsqc_2dsequences" value="yes"/> - <param name="tocsy_2dsequences" value="no"/> - <param name="tocsy_2dsequences" value="no"/> - <param name="inHouse_DB_choices.choice" value="no"/> - <param name="tolppm1" value="0.01"/> - <param name="tolppm2" value="0.5"/> - <param name="tolppmJRES" value="0.002"/> - <param name="threshold" value="0.3"/> - <param name="unicity" value="no"/> - <output name="annotationJRES" file="annotationJres.tabular"/> - <output name="ppmCommunJRES" file="duplicateJres.tabular"/> - <output name="annotationHSQC" file="annotationHsqc.tabular"/> - <output name="ppmCommunHSQC" file="duplicateHsqc.tabular"/> - <output name="annotationCombination" file="2DNMR_Annotation_annotationCombination.tabular"/> - </test> - </tests> -<help> + <test expect_num_outputs="13"> + <param name="zip_xlsfile" value="Template_melange.xlsx" ftype="xlsx"/> + <param name="cosy_2dsequences" value="yes"/> + <param name="jres_2dsequences" value="yes"/> + <param name="hmbc_2dsequences" value="yes"/> + <param name="hsqc_2dsequences" value="yes"/> + <param name="tocsy_2dsequences" value="yes"/> + <param name="inHouse_DB_choices.choice" value="no"/> + <param name="tolppm1" value="0.01"/> + <param name="tolppm2" value="0.5"/> + <param name="tolppmJRES" value="0.002"/> + <param name="threshold" value="0.3"/> + <param name="unicity" value="no"/> + <output name="annotationCOSY" file="2DNMRAnnotation_annotationCOSY.tabular"/> + <output name="ppmCommunCOSY" file="2DNMRAnnotation_duplicateCOSY.tabular"/> + <output name="annotationHMBC" file="2DNMRAnnotation_annotationHMBC.tabular"/> + <output name="ppmCommunHMBC" file="2DNMRAnnotation_duplicateHMBC.tabular"/> + <output name="annotationHSQC" file="2DNMRAnnotation_annotationHSQC.tabular"/> + <output name="ppmCommunHSQC" file="2DNMRAnnotation_duplicateHSQC.tabular"/> + <output name="annotationJRES" file="2DNMRAnnotation_annotationJRES.tabular"/> + <output name="ppmCommunJRES" file="2DNMRAnnotation_duplicateJRES.tabular"/> + <output name="annotationTOCSY" file="2DNMRAnnotation_annotationTOCSY.tabular"/> + <output name="ppmCommunTOCSY" file="2DNMRAnnotation_duplicateTOCSY.tabular"/> + <output name="annotationCombination" file="2DNMRAnnotation_annotationCombination.tabular"/> + </test> + </tests> + <help> .. class:: infomark