# HG changeset patch
# User workflow4metabolomics
# Date 1752222807 0
# Node ID e2b63e0c04e152222111c7ad37e3afbc241f4f7b
# Parent cf11fa0c47c8364231da48a55e586ca69f9dfcbe
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 3d328007dd7716848ec2eeb6c2a472f27eeb2995
diff -r cf11fa0c47c8 -r e2b63e0c04e1 annotationRmn2D.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/annotationRmn2D.xml Fri Jul 11 08:33:27 2025 +0000
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+
+ Annotation of complex mixture bidimensional NMR spectra
+
+
+ r-batch
+ r-dplyr
+ r-ggplot2
+ r-openxlsx
+ r-stringr
+ r-tidyr
+ r-curl
+ r-jsonlite
+ r-stringi
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+ cosy_2dsequences != "no"
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+ cosy_2dsequences != "no"
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+ jres_2dsequences != "no"
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+ jres_2dsequences != "no"
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+ hmbc_2dsequences != "no"
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+ hmbc_2dsequences != "no"
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+ hsqc_2dsequences != "no"
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+ hsqc_2dsequences != "no"
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+ tocsy_2dsequences != "no"
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+ tocsy_2dsequences != "no"
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+.. class:: infomark
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+**Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Coline Gardou
+
+.. class:: infomark
+
+
+---------------------------------------------------
+
+============================
+Bidimensional NMR Annotation
+============================
+
+-----------
+Description
+-----------
+
+BARSA is an automatic algorithm for bi-dimensional NMR spectra annotation
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+========================= ================= ======= =========
+Name output file format parameter
+========================= ================= ======= =========
+NA NA NA NA
+========================= ================= ======= =========
+
+
+**Downstream tools**
+
+========================= ================= ======= =========
+Name output file format parameter
+========================= ================= ======= =========
+NA NA NA NA
+========================= ================= ======= =========
+
+
+
+-----------
+Input files
+-----------
+
++---------------------------+------------+
+| Parameter : num + label | Format |
++===========================+============+
+| 1 : Choose your inputs | xlsx |
++---------------------------+------------+
+
+**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
+ | HMBC: yes/no
+ | HSQC: yes/no
+ | TOCSY: yes/no
+ | Default value is no
+ |
+
+In-house databases
+ | 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
+ |
+
+
+Threshold
+ | All metabolites with a presence probability (number of detected peak(s)/number of theoretical peak(s)) under this threshold are removed
+ | Default value: 0
+ |
+
+
+Unicity of annotation
+ | All the peaks assigned to more than one metabolite are removed
+ |
+
+
+------------
+Output files
+------------
+COSY
+ | tabular outputs
+ | annotationCOSY: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
+ | ppmCommunCOSY: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
+ | Only display if COSY was chosen
+ |
+
+
+JRES
+ | tabular outputs
+ | annotationJRES: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
+ | ppmCommunJRES: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
+ | Only display if JRES was chosen
+ |
+
+
+HMBC
+ | tabular outputs
+ | annotationHMBC: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
+ | ppmCommunHMBC: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
+ | Only display if HMBC was chosen
+ |
+
+
+HSQC
+ | tabular outputs
+ | annotationHSQC: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
+ | ppmCommunHSQC: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
+ | Only display if HSQC was chosen
+ |
+
+
+TOCSY
+ | tabular outputs
+ | annotationTOCSY: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
+ | ppmCommunTOCSY: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
+ | Only display if TOCSY was chosen
+ |
+
+
+annotationCombination
+ | tabular outputs
+ | Array with p rows (corresponding to the identified metabolites) including the Metabolite name, the COSY presence probability, the JRES presence probability, the HMBC presence probability, the HSQC presence probability, the TOCSY presence probability and the averageScore
+ | Depends on the chosen sequences
+ | Only display if 2 or more sequences have be chosen
+
+
+AnnotationGraph.pdf
+ | pdf output
+ | Bi-dimensional graphical chart of real pairs of chemical shifts, with name of identified metabolites
+
+
+
+---------------------------------------------------
+
+-------
+Example
+-------
+Example of output files obtaining wehn running the algorithm on a mix of 23 known compounds
+
+.. image:: ./static/images/OutputsExampleMix.png
+ :width: 500
+
+
+
+ 10.1093/bioinformatics/btu813
+
+
diff -r cf11fa0c47c8 -r e2b63e0c04e1 annotationRmn2D_xml.xml
--- a/annotationRmn2D_xml.xml Thu Jan 23 15:28:44 2025 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,442 +0,0 @@
-
-
- Annotation of complex mixture bidimensional NMR spectra
-
-
- r-batch
- r-dplyr
- r-ggplot2
- r-openxlsx
- r-stringr
- r-tidyr
- r-curl
- r-jsonlite
- r-stringi
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- cosy_2dsequences != "no"
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- cosy_2dsequences != "no"
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- jres_2dsequences != "no"
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- jres_2dsequences != "no"
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- hmbc_2dsequences != "no"
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- hmbc_2dsequences != "no"
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- hsqc_2dsequences != "no"
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- hsqc_2dsequences != "no"
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- tocsy_2dsequences != "no"
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-.. class:: infomark
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-**Authors** Marie Tremblay-Franco (marie.tremblay-franco@inra.fr), Coline Gardou
-
-.. class:: infomark
-
-
----------------------------------------------------
-
-============================
-Bidimensional NMR Annotation
-============================
-
------------
-Description
------------
-
-BARSA is an automatic algorithm for bi-dimensional NMR spectra annotation
-
------------------
-Workflow position
------------------
-
-**Upstream tools**
-
-========================= ================= ======= =========
-Name output file format parameter
-========================= ================= ======= =========
-NA NA NA NA
-========================= ================= ======= =========
-
-
-**Downstream tools**
-
-========================= ================= ======= =========
-Name output file format parameter
-========================= ================= ======= =========
-NA NA NA NA
-========================= ================= ======= =========
-
-
-
------------
-Input files
------------
-
-+---------------------------+------------+
-| Parameter : num + label | Format |
-+===========================+============+
-| 1 : Choose your inputs | xlsx |
-+---------------------------+------------+
-
-**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
- | HMBC: yes/no
- | HSQC: yes/no
- | TOCSY: yes/no
- | Default value is no
- |
-
-In-house databases
- | 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
- |
-
-
-Threshold
- | All metabolites with a presence probability (number of detected peak(s)/number of theoretical peak(s)) under this threshold are removed
- | Default value: 0
- |
-
-
-Unicity of annotation
- | All the peaks assigned to more than one metabolite are removed
- |
-
-
-------------
-Output files
-------------
-COSY
- | tabular outputs
- | annotationCOSY: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
- | ppmCommunCOSY: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
- | Only display if COSY was chosen
- |
-
-
-JRES
- | tabular outputs
- | annotationJRES: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
- | ppmCommunJRES: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
- | Only display if JRES was chosen
- |
-
-
-HMBC
- | tabular outputs
- | annotationHMBC: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
- | ppmCommunHMBC: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
- | Only display if HMBC was chosen
- |
-
-
-HSQC
- | tabular outputs
- | annotationHSQC: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
- | ppmCommunHSQC: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
- | Only display if HSQC was chosen
- |
-
-
-TOCSY
- | tabular outputs
- | annotationTOCSY: Array with p rows (corresponding to the identified metabolites) and 4 columns containing the chemical shift on the x-axis, the chemical shift on the y-axis, the metabolite name and the presence probability
- | ppmCommunTOCSY: Array containing for all the peaks assigned to more than one metabolite: the chemical shift on the x-axis, the chemical shift on the y-axis and the list of assigned metabolites
- | Only display if TOCSY was chosen
- |
-
-
-annotationCombination
- | tabular outputs
- | Array with p rows (corresponding to the identified metabolites) including the Metabolite name, the COSY presence probability, the JRES presence probability, the HMBC presence probability, the HSQC presence probability, the TOCSY presence probability and the averageScore
- | Depends on the chosen sequences
- | Only display if 2 or more sequences have be chosen
-
-
-AnnotationGraph.pdf
- | pdf output
- | Bi-dimensional graphical chart of real pairs of chemical shifts, with name of identified metabolites
-
-
-
----------------------------------------------------
-
--------
-Example
--------
-Example of output files obtaining wehn running the algorithm on a mix of 23 known compounds
-
-.. image:: ./static/images/OutputsExampleMix.png
- :width: 500
-
-
-
- 10.1093/bioinformatics/btu813
-
-
-