# HG changeset patch
# User marie-tremblay-metatoul
# Date 1580807138 18000
# Node ID a4d2b1926e132a37be8b4fc7f00e00225f759490
# Parent  8035235e46c7a5c3472e6ae63a8f5c521970641b
Uploaded

diff -r 8035235e46c7 -r a4d2b1926e13 nmr_annotation2d/.shed.yml
--- a/nmr_annotation2d/.shed.yml	Mon Dec 23 09:26:20 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-categories: [Metabolomics]
-description: '[Metabolomics][W4M][NMR] BARSA - BidimensionAl nmR Spectra Annotation'
-homepage_url: http://workflow4metabolomics.org
-long_description: 'Part of the W4M project: http://workflow4metabolomics.org'
-name: 2DNmrAnnotation
-owner: marie-tremblay-metatoul
-remote_repository_url: https://github.com/workflow4metabolomics/nmr_annotation2d
diff -r 8035235e46c7 -r a4d2b1926e13 nmr_annotation2d/.travis.yml
--- a/nmr_annotation2d/.travis.yml	Mon Dec 23 09:26:20 2019 -0500
+++ b/nmr_annotation2d/.travis.yml	Tue Feb 04 04:05:38 2020 -0500
@@ -1,17 +1,20 @@
-
 # This is a special configuration file to run tests on Travis-CI via
 # GitHub notifications when changes are committed.
 #
 # See http://travis-ci.org/ for details
 language: python
 
+env:
+  - TESTFOLDER=.
+
 before_install:
+  - export GALAXY_RELEASE=release_19.05
+
+install:
  - sudo apt-get install -y python-virtualenv
- - virtualenv planemo-venv
- - . planemo-venv/bin/activate
- - pip install --upgrade pip setuptools
- - pip install planemo==0.37.0
+ - sudo pip install planemo==0.58.1
+  
+script:
+ - planemo lint ${TRAVIS_BUILD_DIR}/${TESTFOLDER}
+ - planemo test --galaxy_branch $GALAXY_RELEASE  --galaxy_source "$GALAXY_REPO" --no_cache_galaxy ${TRAVIS_BUILD_DIR}/${TESTFOLDER}
 
-script:
- - planemo lint ${TRAVIS_BUILD_DIR}/galaxy/2DNmrAnnotation/
-# - planemo test --conda_auto_init --conda_auto_install --conda_dependency_resolution --galaxy_branch release_17.01 --no_cache_galaxy ${TRAVIS_BUILD_DIR}/galaxy/2DNmrAnnotation/
diff -r 8035235e46c7 -r a4d2b1926e13 nmr_annotation2d/README.md.rej
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_annotation2d/README.md.rej	Tue Feb 04 04:05:38 2020 -0500
@@ -0,0 +1,4 @@
+diff a/README.md b/README.md	(rejected hunks)
+@@ -0,0 +1,2 @@
++# nmr_annotation2d
++Algorithm for automated annotation of bi-dimensional NMR spectre (BARSA)
diff -r 8035235e46c7 -r a4d2b1926e13 nmr_annotation2d/annotationRmn2D_xml.xml
--- 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>
diff -r 8035235e46c7 -r a4d2b1926e13 nmr_annotation2d/test-data/annotationHsqc.tabular
--- a/nmr_annotation2d/test-data/annotationHsqc.tabular	Mon Dec 23 09:26:20 2019 -0500
+++ b/nmr_annotation2d/test-data/annotationHsqc.tabular	Tue Feb 04 04:05:38 2020 -0500
@@ -1,77 +1,77 @@
-ppm1	ppm2	Metabolite	score
-1.487	19.022	alanine	1
-3.791	53.343	alanine	1
-2.883	37.372	asparagine	1
-2.964	37.382	asparagine	1
-4.016	54.04	asparagine	1
-2.694	39.367	Aspartic_acid	1
-2.816	39.387	Aspartic_acid	1
-3.905	54.962	Aspartic_acid	1
-3.264	56.272	betaine	1
-3.901	69.074	betaine	1
-2.164	42.369	Butyric acid	0.333333333333333
-3.024	41.961	Cadaverine	0.333333333333333
-2.444	45.792	carnitine	1
-3.232	56.932	carnitine	1
-3.44	72.954	carnitine	1
-4.571	66.903	carnitine	1
-3.208	56.704	CholineChloride	0.666666666666667
-4.072	58.227	CholineChloride	0.666666666666667
-6.526	138.157	Fumaric acid	1
-3.015	42.093	gaba	0.333333333333333
-3.502	74.756	galactose	0.833333333333333
-3.661	75.593	galactose	0.833333333333333
-3.717	78.019	galactose	0.833333333333333
-3.815	71.175	galactose	0.833333333333333
-3.866	71.993	galactose	0.833333333333333
-3.942	71.619	galactose	0.833333333333333
-4	72.162	galactose	0.833333333333333
-4.096	73.292	galactose	0.833333333333333
-4.598	99.277	galactose	0.833333333333333
-5.277	95.132	galactose	0.833333333333333
-3.425	72.307	glucose	0.666666666666667
-3.46	78.647	glucose	0.666666666666667
-3.549	74.169	glucose	0.666666666666667
-3.745	63.514	glucose	0.666666666666667
-3.841	74.223	glucose	0.666666666666667
-3.847	63.4	glucose	0.666666666666667
-4.66	98.737	glucose	0.666666666666667
-5.252	94.768	glucose	0.666666666666667
-3.566	44.267	glycine	1
-3.967	46.611	hippuric_acid	1
-7.556	131.578	hippuric_acid	1
-7.643	135.065	hippuric_acid	1
-7.837	130.019	hippuric_acid	1
-3.209	30.164	Histidine	1
-3.29	30.194	Histidine	1
-4.014	57.269	Histidine	1
-7.155	119.969	Histidine	1
-8.04	138.39	Histidine	1
-0.944	14.001	Isoleucine	1
-1.017	17.526	Isoleucine	1
-1.27	27.262	Isoleucine	1
-1.479	27.34	Isoleucine	1
-1.987	38.709	Isoleucine	1
-3.68	62.433	Isoleucine	1
-1.336	22.913	Lactic acid	1
-4.12	71.318	Lactic acid	1
-2.009	26.543	Proline	1
-2.062	31.789	Proline	1
-2.357	31.817	Proline	1
-3.346	48.831	Proline	1
-3.422	48.867	Proline	1
-4.14	63.947	Proline	1
-1.342	22.349	threonine	1
-3.609	63.354	threonine	1
-4.261	68.825	threonine	1
-3.321	29.248	tryptophan	1
-3.492	29.268	tryptophan	1
-4.066	57.824	tryptophan	1
-7.209	122.251	tryptophan	1
-7.292	124.963	tryptophan	1
-7.337	127.891	tryptophan	1
-7.554	114.838	tryptophan	1
-7.743	121.238	tryptophan	1
-1	19.497	valine	0.75
-1.049	20.77	valine	0.75
-2.281	31.893	valine	0.75
+ppm1	ppm2	Metabolite	score
+1.487	19.022	alanine	1
+3.791	53.343	alanine	1
+2.883	37.372	asparagine	1
+2.964	37.382	asparagine	1
+4.016	54.04	asparagine	1
+2.694	39.367	Aspartic_acid	1
+2.816	39.387	Aspartic_acid	1
+3.905	54.962	Aspartic_acid	1
+3.264	56.272	betaine	1
+3.901	69.074	betaine	1
+2.164	42.369	Butyric acid	0.333333333333333
+3.024	41.961	Cadaverine	0.333333333333333
+2.444	45.792	carnitine	1
+3.232	56.932	carnitine	1
+3.44	72.954	carnitine	1
+4.571	66.903	carnitine	1
+3.208	56.704	CholineChloride	0.666666666666667
+4.072	58.227	CholineChloride	0.666666666666667
+6.526	138.157	Fumaric acid	1
+3.015	42.093	gaba	0.333333333333333
+3.502	74.756	galactose	0.833333333333333
+3.661	75.593	galactose	0.833333333333333
+3.717	78.019	galactose	0.833333333333333
+3.815	71.175	galactose	0.833333333333333
+3.866	71.993	galactose	0.833333333333333
+3.942	71.619	galactose	0.833333333333333
+4	72.162	galactose	0.833333333333333
+4.096	73.292	galactose	0.833333333333333
+4.598	99.277	galactose	0.833333333333333
+5.277	95.132	galactose	0.833333333333333
+3.425	72.307	glucose	0.666666666666667
+3.46	78.647	glucose	0.666666666666667
+3.549	74.169	glucose	0.666666666666667
+3.745	63.514	glucose	0.666666666666667
+3.841	74.223	glucose	0.666666666666667
+3.847	63.4	glucose	0.666666666666667
+4.66	98.737	glucose	0.666666666666667
+5.252	94.768	glucose	0.666666666666667
+3.566	44.267	glycine	1
+3.967	46.611	hippuric_acid	1
+7.556	131.578	hippuric_acid	1
+7.643	135.065	hippuric_acid	1
+7.837	130.019	hippuric_acid	1
+3.209	30.164	Histidine	1
+3.29	30.194	Histidine	1
+4.014	57.269	Histidine	1
+7.155	119.969	Histidine	1
+8.04	138.39	Histidine	1
+0.944	14.001	Isoleucine	1
+1.017	17.526	Isoleucine	1
+1.27	27.262	Isoleucine	1
+1.479	27.34	Isoleucine	1
+1.987	38.709	Isoleucine	1
+3.68	62.433	Isoleucine	1
+1.336	22.913	Lactic acid	1
+4.12	71.318	Lactic acid	1
+2.009	26.543	Proline	1
+2.062	31.789	Proline	1
+2.357	31.817	Proline	1
+3.346	48.831	Proline	1
+3.422	48.867	Proline	1
+4.14	63.947	Proline	1
+1.342	22.349	threonine	1
+3.609	63.354	threonine	1
+4.261	68.825	threonine	1
+3.321	29.248	tryptophan	1
+3.492	29.268	tryptophan	1
+4.066	57.824	tryptophan	1
+7.209	122.251	tryptophan	1
+7.292	124.963	tryptophan	1
+7.337	127.891	tryptophan	1
+7.554	114.838	tryptophan	1
+7.743	121.238	tryptophan	1
+1	19.497	valine	0.75
+1.049	20.77	valine	0.75
+2.281	31.893	valine	0.75
diff -r 8035235e46c7 -r a4d2b1926e13 nmr_annotation2d/viridis.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nmr_annotation2d/viridis.R	Tue Feb 04 04:05:38 2020 -0500
@@ -0,0 +1,28 @@
+viridis <- function (n, alpha = 1, begin = 0, end = 1, direction = 1, option = "D") 
+{
+  if (begin < 0 | begin > 1 | end < 0 | end > 1) {
+    stop("begin and end must be in [0,1]")
+  }
+  if (abs(direction) != 1) {
+    stop("direction must be 1 or -1")
+  }
+  if (direction == -1) {
+    tmp <- begin
+    begin <- end
+    end <- tmp
+  }
+  option <- switch(EXPR = option, A = "A", magma = "A", 
+                   B = "B", inferno = "B", C = "C", plasma = "C", 
+                   D = "D", viridis = "D", E = "E", cividis = "E", 
+                   {
+                     warning(paste0("Option '", option, "' does not exist. Defaulting to 'viridis'."))
+                     "D"
+                   })
+  map <- viridisLite::viridis.map[viridisLite::viridis.map$opt == 
+                                    option, ]
+  map_cols <- grDevices::rgb(map$R, map$G, map$B)
+  fn_cols <- grDevices::colorRamp(map_cols, space = "Lab", 
+                                  interpolate = "spline")
+  cols <- fn_cols(seq(begin, end, length.out = n))/255
+  grDevices::rgb(cols[, 1], cols[, 2], cols[, 3], alpha = alpha)
+}
\ No newline at end of file