Mercurial > repos > marie-tremblay-metatoul > 2dnmrannotation
diff nmr_annotation2d/annotationRmn2D_xml.xml @ 1:a4d2b1926e13 draft
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| author | marie-tremblay-metatoul |
|---|---|
| date | Tue, 04 Feb 2020 04:05:38 -0500 |
| parents | 8035235e46c7 |
| children |
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--- a/nmr_annotation2d/annotationRmn2D_xml.xml Mon Dec 23 09:26:20 2019 -0500 +++ b/nmr_annotation2d/annotationRmn2D_xml.xml Tue Feb 04 04:05:38 2020 -0500 @@ -1,172 +1,188 @@ <tool id="2DNmrAnnotation" name="2DNMR_Annotation" version="1.0.0"> - - <description> Annotation of complex mixture bidimensional NMR spectra </description> + + <description> Annotation of complex mixture bidimensional NMR spectra </description> + + <requirements> + <requirement type="package" version="1.1_5">r-batch</requirement> + <requirement type="package" version="0.8.3">r-dplyr</requirement> + <requirement type="package" version="3.2.1">r-ggplot2</requirement> + <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> + </requirements> <stdio> <exit_code range="1:" level="fatal" /> - </stdio> + </stdio> + + <command> + ## Wrapper + Libraries of 2D-NMR sequences for reference compounds + Rscript '$__tool_directory__/annotationRmn2DWrapper.R' + + + ## XLS file + xlsfile '$zip_xlsfile' + + ## 2D-NMR sequences to annotate + cosy_2dsequences $cosy_2dsequences + jres_2dsequences $jres_2dsequences + hmbc_2dsequences $hmbc_2dsequences + hsqc_2dsequences $hsqc_2dsequences + tocsy_2dsequences $tocsy_2dsequences - <command> - ## Wrapper + Libraries of 2D-NMR sequences for reference compounds - Rscript '$__tool_directory__/annotationRmn2DWrapper.R' + ## In-house databases + inHouse_DB_choices.choice ${inHouse_DB_choices.choice} + #if str($inHouse_DB_choices.choice) == 'yes': + inHouse_DB_cosy.choice ${inHouse_DB_choices.inHouse_DB_cosy.choice} + #if str($inHouse_DB_choices.inHouse_DB_cosy.choice) == 'yes': + cosyDB $inHouse_DB_choices.inHouse_DB_cosy.cosyDB + #end if + inHouse_DB_hmbc.choice ${inHouse_DB_choices.inHouse_DB_hmbc.choice} + #if str($inHouse_DB_choices.inHouse_DB_hmbc.choice) == 'yes': + hmbcDB $inHouse_DB_choices.inHouse_DB_hmbc.hmbcDB + #end if + inHouse_DB_hsqc.choice ${inHouse_DB_choices.inHouse_DB_hsqc.choice} + #if str($inHouse_DB_choices.inHouse_DB_hsqc.choice) == 'yes': + hsqcDB $inHouse_DB_choices.inHouse_DB_hsqc.hsqcDB + #end if + inHouse_DB_jres.choice ${inHouse_DB_choices.inHouse_DB_jres.choice} + #if str($inHouse_DB_choices.inHouse_DB_jres.choice) == 'yes': + jresDB $inHouse_DB_choices.inHouse_DB_jres.jresDB + #end if + inHouse_DB_tocsy.choice ${inHouse_DB_choices.inHouse_DB_tocsy.choice} + #if str($inHouse_DB_choices.inHouse_DB_tocsy.choice) == 'yes': + tocsyDB $inHouse_DB_choices.inHouse_DB_tocsy.tocsyDB + #end if + #end if + + ## Tolerances + tolppm1 $tolppm1 + tolppm2 $tolppm2 + tolppmJRES $tolppmJRES - ## XLS file - xlsfile $zip_xlsfile + ## Treshold (probability score) + threshold $threshold + + ## Unicity + unicity $unicity + + ## Outputs + logOut '$logOut' + annotationCOSY '$annotationCOSY' + ppmCommunCOSY '$ppmCommunCOSY' + annotationJRES '$annotationJRES' + ppmCommunJRES '$ppmCommunJRES' + annotationHMBC '$annotationHMBC' + ppmCommunHMBC '$ppmCommunHMBC' + annotationHSQC '$annotationHSQC' + ppmCommunHSQC '$ppmCommunHSQC' + annotationTOCSY '$annotationTOCSY' + ppmCommunTOCSY '$ppmCommunTOCSY' + annotationCombination '$annotationCombination' + AnnotationGraph '$AnnotationGraph' + + </command> - ## 2D-NMR sequences to annotate - cosy_2dsequences $cosy_2dsequences - jres_2dsequences $jres_2dsequences - hmbc_2dsequences $hmbc_2dsequences - hsqc_2dsequences $hsqc_2dsequences - tocsy_2dsequences $tocsy_2dsequences - - ## In-house databases - inHouse_DB_choices.choice ${inHouse_DB_choices.choice} - #if str($inHouse_DB_choices.choice) == 'yes': - inHouse_DB_cosy.choice ${inHouse_DB_cosy.choice} - #if str($inHouse_DB_cosy.choice) == 'yes': - cosyDB $cosyDB - #end if - inHouse_DB_hmbc.choice ${inHouse_DB_hmbc.choice} - #if str($inHouse_DB_hmbc.choice) == 'yes': - hmbcDB $hmbcDB - #end if - inHouse_DB_hsqc.choice ${inHouse_DB_hsqc.choice} - #if str($inHouse_DB_hsqc.choice) == 'yes': - hsqcDB $hsqcDB - #end if - inHouse_DB_jres.choice ${inHouse_DB_jres.choice} - #if str($inHouse_DB_jres.choice) == 'yes': - jresDB $jresDB - #end if - inHouse_DB_tocsy.choice ${inHouse_DB_tocsy.choice} - #if str($inHouse_DB_tocsy.choice) == 'yes': - tocsyDB $tocsyDB - #end if - #end if + <inputs> + <param name="zip_xlsfile" type="data" format="xlsx" label="File to annotate in xlsx format" /> - ## Tolerances - tolppm1 $tolppm1 - tolppm2 $tolppm2 - tolppmJRES $tolppmJRES - - - ## Treshold (probability score) - threshold $threshold - - ## Unicity - unicity $unicity - - ## Outputs - logOut $logOut - annotationCOSY $annotationCOSY - ppmCommunCOSY $ppmCommunCOSY - annotationJRES $annotationJRES - ppmCommunJRES $ppmCommunJRES - annotationHMBC $annotationHMBC - ppmCommunHMBC $ppmCommunHMBC - annotationHSQC $annotationHSQC - ppmCommunHSQC $ppmCommunHSQC - annotationTOCSY $annotationTOCSY - 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="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> + </param> + <param name="hsqc_2dsequences" type="select" label="2D-NMR HSQC 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> + </param> - <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> - </param> - <param name="hsqc_2dsequences" type="select" label="2D-NMR HSQC 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> - </param> - - <conditional name="inHouse_DB_choices"> - <param name="choice" type="select" label="In-house database" help="Choose if you want to use use in-house database to annotate" > - <option value="yes" > yes </option> - <option value="no" selected="true"> no </option> - </param> - <when value="yes"> - <conditional name="inHouse_DB_cosy"> - <param name="choice" type="select" label="COSY In-house database" help="Choose if you want to use use in-house database to annotate COSY sequence" > - <option value="yes" > yes </option> - <option value="no" selected="true"> no </option> - </param> - <when value="yes"> - <param name="cosyDB" type="data" format="no_unzip.zip" label="Zip file of the COSY RData object" /> - </when> - </conditional> - <conditional name="inHouse_DB_hmbc"> - <param name="choice" type="select" label="HMBC In-house database" help="Choose if you want to use use in-house database to annotate HMBC sequence" > - <option value="yes" > yes </option> - <option value="no" selected="true"> no </option> - </param> - <when value="yes"> - <param name="hmbcDB" type="data" format="no_unzip.zip" label="Zip file of the HMBC RData object" /> - </when> - </conditional> <conditional name="inHouse_DB_hsqc"> - <param name="choice" type="select" label="HSQC In-house database" help="Choose if you want to use use in-house database to annotate HSQC sequence" > - <option value="yes" > yes </option> - <option value="no" selected="true"> no </option> - </param> - <when value="yes"> - <param name="hsqcDB" type="data" format="no_unzip.zip" label="Zip file of the HSQC RData object" /> - </when> - </conditional> <conditional name="inHouse_DB_jres"> - <param name="choice" type="select" label="JRES In-house database" help="Choose if you want to use use in-house database to annotate JRES sequence" > - <option value="yes" > yes </option> - <option value="no" selected="true"> no </option> - </param> - <when value="yes"> - <param name="jresDB" type="data" format="no_unzip.zip" label="Zip file of the JRES RData object" /> - </when> - </conditional> - <conditional name="inHouse_DB_tocsy"> - <param name="choice" type="select" label="TOCSY In-house database" help="Choose if you want to use use in-house database to annotate TOCSY sequence" > - <option value="yes" > yes </option> - <option value="no" selected="true"> no </option> - </param> - <when value="yes"> - <param name="tocsyDB" type="data" format="no_unzip.zip" label="Zip file of the TOCSY RData object" /> - </when> - </conditional> - </when> - <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)" /> + <conditional name="inHouse_DB_choices"> + <param name="choice" type="select" label="In-house database" help="Choose if you want to use use in-house database to annotate" > + <option value="yes" > yes </option> + <option value="no" selected="true"> no </option> + </param> + <when value="yes"> + <conditional name="inHouse_DB_cosy"> + <param name="choice" type="select" label="COSY In-house database" help="Choose if you want to use use in-house database to annotate COSY sequence" > + <option value="yes" > yes </option> + <option value="no" selected="true"> no </option> + </param> + <when value="yes"> + <param name="cosyDB" type="data" format="no_unzip.zip" label="Zip file of the COSY RData object" /> + </when> + <when value="no" /> + </conditional> + <conditional name="inHouse_DB_hmbc"> + <param name="choice" type="select" label="HMBC In-house database" help="Choose if you want to use use in-house database to annotate HMBC sequence" > + <option value="yes" > yes </option> + <option value="no" selected="true"> no </option> + </param> + <when value="yes"> + <param name="hmbcDB" type="data" format="no_unzip.zip" label="Zip file of the HMBC RData object" /> + </when> + <when value="no" /> + </conditional> + <conditional name="inHouse_DB_hsqc"> + <param name="choice" type="select" label="HSQC In-house database" help="Choose if you want to use use in-house database to annotate HSQC sequence" > + <option value="yes" > yes </option> + <option value="no" selected="true"> no </option> + </param> + <when value="yes"> + <param name="hsqcDB" type="data" format="no_unzip.zip" label="Zip file of the HSQC RData object" /> + </when> + <when value="no" /> + </conditional> + <conditional name="inHouse_DB_jres"> + <param name="choice" type="select" label="JRES In-house database" help="Choose if you want to use use in-house database to annotate JRES sequence" > + <option value="yes" > yes </option> + <option value="no" selected="true"> no </option> + </param> + <when value="yes"> + <param name="jresDB" type="data" format="no_unzip.zip" label="Zip file of the JRES RData object" /> + </when> + <when value="no" /> + </conditional> + <conditional name="inHouse_DB_tocsy"> + <param name="choice" type="select" label="TOCSY In-house database" help="Choose if you want to use use in-house database to annotate TOCSY sequence" > + <option value="yes" > yes </option> + <option value="no" selected="true"> no </option> + </param> + <when value="yes"> + <param name="tocsyDB" type="data" format="no_unzip.zip" label="Zip file of the TOCSY RData object" /> + </when> + <when value="no" /> + </conditional> + </when> + <when value="no" /> + </conditional> - <param name="threshold" type="float" value="0" help="Treshold on score of presence. Default value is 0" /> + <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="threshold" type="float" value="0" help="Treshold on score of presence. Default value is 0" /> - <param name="unicity" label="Unicity of annotation" type="select" display="radio" help=""> - <option value="no">No</option> - <option value="yes"></option> - </param> + <param name="unicity" label="Unicity of annotation" type="select" display="radio" help=""> + <option value="no">No</option> + <option value="yes"></option> + </param> - </inputs> + </inputs> - <outputs> - <data format="txt" name="logOut" label="${tool.name}_log" /> + <outputs> + <data format="txt" name="logOut" label="${tool.name}_log" /> <data format="tabular" name="annotationCOSY" label="annotationCosy" > <filter> cosy_2dsequences != "no" </filter> </data> @@ -203,9 +219,30 @@ </data> <data format="tabular" name="annotationCombination" label="${tool.name}_annotationCombination" /> - <data format="pdf" name="AnnotationGraph" label="${tool.name}_graph" /> - </outputs> - + <data format="pdf" name="AnnotationGraph" label="${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> .. class:: infomark @@ -226,7 +263,7 @@ ----------- BARSA is an automatic algorithm for bi-dimensional NMR spectra annotation - + ----------------- Workflow position ----------------- @@ -236,7 +273,7 @@ ========================= ================= ======= ========= Name output file format parameter ========================= ================= ======= ========= -NA NA NA NA +NA NA NA NA ========================= ================= ======= ========= @@ -245,7 +282,7 @@ ========================= ================= ======= ========= Name output file format parameter ========================= ================= ======= ========= -NA NA NA NA +NA NA NA NA ========================= ================= ======= ========= @@ -263,13 +300,13 @@ **Choose your inputs** | xlsx file can include several peak lists, coming from several 2D NMR sequences | - + .. image:: ./static/images/2DNmr_FileToAnnotate_xlsxFormat.png ---------- Parameters ---------- - + Bi-dimensional NMR peak list(s) to annotate; select one or more sequence(s) | COSY: yes/no | JRES: yes/no @@ -283,14 +320,14 @@ | Use of your own databases to annotate peak list(s) | If YES: parameters **COSY In-house database**, **JRES In-house database**, ** HMBC In-house database**, **HSQC In-house database** and **TOCSY In-house database** are visible | Select one or more in-house database - | + | Tolerances | tolppm1: Maximum variation of the chemical shift (due to experimental conditions) of a peak along the x-axis | tolppm2: Maximum variation of the chemical shift (due to experimental conditions) of a peak along the y-axis | tolppmJRES: Maximum variation of the chemical shift (due to experimental conditions) of a peak for the JRES sequence - | Default values: 0.01 and 0.01 ppm; 0.002 Hz + | Default values: 0.01 and 0.01 ppm; 0.002 Hz | @@ -358,7 +395,7 @@ AnnotationGraph.pdf | pdf output | Bi-dimensional graphical chart of real pairs of chemical shifts, with name of identified metabolites - + --------------------------------------------------- @@ -370,7 +407,10 @@ .. image:: ./static/images/OutputsExampleMix.png :width: 500 - - </help> - + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + </tool>