# HG changeset patch
# User workflow4metabolomics
# Date 1589315968 14400
# Node ID db6549f27ad12844b96822abf6bdb0938ca143bd
# Parent  acc66e5c23d7d1b75c53e7ea86a5d11191c4e922
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 7234c5fb8350990733e882693248c0433eee5ff8"

diff -r acc66e5c23d7 -r db6549f27ad1 README.rst
--- a/README.rst	Wed Feb 12 08:30:41 2020 -0500
+++ b/README.rst	Tue May 12 16:39:28 2020 -0400
@@ -4,6 +4,12 @@
 
 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
+**Version 3.6.1+galaxy1 - 05/04/2020**
+
+- UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0
+
+- BUGFIX: "Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds"
+
 **Version 3.6.1.0 - 03/09/2019**
 
 - UPGRADE: upgrade the xcms version from 3.4.4 to 3.6.1 (see XCMS News_)
diff -r acc66e5c23d7 -r db6549f27ad1 abims_xcms_summary.xml
--- a/abims_xcms_summary.xml	Wed Feb 12 08:30:41 2020 -0500
+++ b/abims_xcms_summary.xml	Tue May 12 16:39:28 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy0">
+<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy1">
 
     <description>Create a summary of XCMS analysis</description>
 
@@ -8,8 +8,9 @@
     </macros>
 
     <requirements>
-        <requirement type="package" version="1.38.1">bioconductor-camera</requirement>
-        <requirement type="package" version="1.1_4">r-batch</requirement>
+	<requirement type="package" version="@TOOL_VERSION@">bioconductor-xcms</requirement>    
+	<requirement type="package" version="1.40.0">bioconductor-camera</requirement>
+        <requirement type="package" version="1.1_5">r-batch</requirement>
     </requirements>
 
     <expand macro="stdio"/>
@@ -88,6 +89,12 @@
 
 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
+**Version 3.6.1+galaxy1 - 05/04/2020**
+
+- UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0
+
+- BUGFIX: "Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds"
+
 @HELP_XCMS_NEWVERSION_3610@
 
 @HELP_XCMS_NEWVERSION_3440@
diff -r acc66e5c23d7 -r db6549f27ad1 lib.r
--- a/lib.r	Wed Feb 12 08:30:41 2020 -0500
+++ b/lib.r	Tue May 12 16:39:28 2020 -0400
@@ -151,12 +151,14 @@
 
     group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
     names(group_colors) <- unique(xdata$sample_group)
+    col_per_samp <- as.character(xdata$sample_group)
+    for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]}
 
     xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
     for (i in 1:nrow(featureDefinitions(xdata))) {
         mzmin = featureDefinitions(xdata)[i,]$mzmin
         mzmax = featureDefinitions(xdata)[i,]$mzmax
-        plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
+        plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=col_per_samp, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
         legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
     }
 
diff -r acc66e5c23d7 -r db6549f27ad1 macros_xcms.xml
--- a/macros_xcms.xml	Wed Feb 12 08:30:41 2020 -0500
+++ b/macros_xcms.xml	Tue May 12 16:39:28 2020 -0400
@@ -98,7 +98,7 @@
                   <option value="maxo">maxo</option>
                   <option value="intb">intb</option>
               </param>
-              <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Replace the remain NA by 0 in the dataMatrix" help="Rather mandatory for some downstream statistical steps"/>
+              <param name="naTOzero" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="If NA values remain, replace them by 0 in the dataMatrix" help="Mandatory for some of the downstream tools (data processing, statistics) that do not accept NA values"/>
     </xml>
 
     <xml name="input_peaklist_section">
@@ -193,7 +193,7 @@
             <option value="wMean">intensity weighted mean of the peak's m/z values</option>
             <option value="mean">mean of the peak's m/z values</option>
             <option value="apex">use the m/z value at the peak apex</option>
-            <option value="wMeanApex3">ntensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
+            <option value="wMeanApex3">intensity weighted mean of the m/z value at the peak apex and the m/z values left and right of it</option>
             <option value="meanApex3">mean of the m/z value of the peak apex and the m/z values left and right of it</option>
         </param>
         <param argument="integrate" type="select" label="Integration method" >
diff -r acc66e5c23d7 -r db6549f27ad1 test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData
Binary file test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData has changed
diff -r acc66e5c23d7 -r db6549f27ad1 test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html
--- a/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html	Wed Feb 12 08:30:41 2020 -0500
+++ b/test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html	Tue May 12 16:39:28 2020 -0400
@@ -16,15 +16,15 @@
 </div>
 <h2>Samples used:</h2>
 <div><table>
-<tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr>
-<tr><td>ko15</td><td>ko15.CDF</td><td>4698c36c0b3af007faf70975c04ccf2a</td></tr><tr><td>ko16</td><td>ko16.CDF</td><td>afaeed94ced3140bc042d5ab6aeb16c1</td></tr><tr><td>wt15</td><td>wt15.CDF</td><td>d58a27fad7c04ddddb0359ddc2b7ba68</td></tr><tr><td>wt16</td><td>wt16.CDF</td><td>29654e9f8ad48c1fbe2a41b9ba578f6e</td></tr>
+<tr><th>sample</th><th>filename</th></tr>
+<tr><td>ko15</td><td>ko15.CDF</td></tr><tr><td>ko16</td><td>ko16.CDF</td></tr><tr><td>wt15</td><td>wt15.CDF</td></tr><tr><td>wt16</td><td>wt16.CDF</td></tr>
 </table>
-<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process.
+
 </div>
 <h2>Function launched:</h2>
 <div><table>
 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
-<tr><td>Wed Feb  7 11:15:25 2018</td><td>Peak detection</td><td colspan='2'><pre>
+<tr><td>Mon May 11 09:37:30 2020</td><td>Peak detection</td><td colspan='2'><pre>
 Object of class:  CentWaveParam 
 Parameters:
  ppm: 25 
@@ -41,17 +41,17 @@
  firstBaselineCheck TRUE 
  roiScales length: 0 
 </pre></td></tr>
-<tr><td>Mon Feb 12 15:31:11 2018</td><td>Peak grouping</td><td colspan='2'><pre>
+<tr><td>Mon May 11 09:37:49 2020</td><td>Peak grouping</td><td colspan='2'><pre>
 Object of class:  PeakDensityParam 
 Parameters:
  sampleGroups: character of length 4 
- bw: 30 
- minFraction: 0.8 
+ bw: 5 
+ minFraction: 0.3 
  minSamples: 1 
- binSize: 0.25 
+ binSize: 0.01 
  maxFeatures: 50 
 </pre></td></tr>
-<tr><td>Mon Feb 12 15:31:19 2018</td><td>Retention time correction</td><td colspan='2'><pre>
+<tr><td>Mon May 11 09:38:08 2020</td><td>Retention time correction</td><td colspan='2'><pre>
 Object of class:  PeakGroupsParam 
 Parameters:
  minFraction: 0.85 
@@ -59,9 +59,10 @@
  smooth: loess 
  span: 0.2 
  family: gaussian 
- number of peak groups: 125 
+ subset:  
+ number of peak groups: 53 
 </pre></td></tr>
-<tr><td>Mon Feb 12 15:31:27 2018</td><td>Peak grouping</td><td colspan='2'><pre>
+<tr><td>Mon May 11 09:38:09 2020</td><td>Peak grouping</td><td colspan='2'><pre>
 Object of class:  PeakDensityParam 
 Parameters:
  sampleGroups: character of length 4 
@@ -71,7 +72,7 @@
  binSize: 0.25 
  maxFeatures: 50 
 </pre></td></tr>
-<tr><td>Wed Feb 14 09:55:13 2018</td><td>Missing peak filling</td><td colspan='2'><pre>
+<tr><td>Mon May 11 09:38:18 2020</td><td>Missing peak filling</td><td colspan='2'><pre>
 Object of class:  FillChromPeaksParam 
 Parameters:
  expandMz: 0 
@@ -84,17 +85,17 @@
 <h2>Informations about the XCMSnExp object:</h2>
 <div><pre>
 MSn experiment data ("XCMSnExp")
-Object size in memory: 1.41 Mb
+Object size in memory: 1.55 Mb
 - - - Spectra data - - -
  MS level(s): 1 
  Number of spectra: 5112 
- MSn retention times: 41:33 - 75:0 minutes
+ MSn retention times: 41:38 - 75:7 minutes
 - - - Processing information - - -
-Concatenated [Thu Feb  8 15:36:09 2018] 
- MSnbase version: 2.4.2 
+Data loaded [Mon May 11 09:37:30 2020] 
+ MSnbase version: 2.10.1 
 - - - Meta data  - - -
 phenoData
-  rowNames: ./ko15.CDF ./ko16.CDF ./wt15.CDF ./wt16.CDF
+  rowNames: 1 2 3 4
   varLabels: sample_name sample_group
   varMetadata: labelDescription
 Loaded from:
@@ -103,31 +104,31 @@
 protocolData: none
 featureData
   featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
-  fvarLabels: fileIdx spIdx ... spectrum (27 total)
+  fvarLabels: fileIdx spIdx ... spectrum (31 total)
   fvarMetadata: labelDescription
 experimentData: use 'experimentData(object)'
 - - - xcms preprocessing - - -
 Chromatographic peak detection:
  method: centWave 
- 15230 peaks identified in 4 samples.
- On average 3808 chromatographic peaks per sample.
+ 15405 peaks identified in 4 samples.
+ On average 3851 chromatographic peaks per sample.
 Alignment/retention time adjustment:
  method: peak groups 
 Correspondence:
  method: chromatographic peak density 
- 6332 features identified.
+ 6349 features identified.
  Median mz range of features: 0
  Median rt range of features: 0
- 5979 filled peaks (on average 1494.75 per sample).
+ 6154 filled peaks (on average 1538.5 per sample).
 </pre></div>
 <h2>Informations about the xcmsSet object:</h2>
 <div><pre>
 An "xcmsSet" object with 4 samples
 
-Time range: 2499.4-4473.6 seconds (41.7-74.6 minutes)
+Time range: 2509.2-4481.8 seconds (41.8-74.7 minutes)
 Mass range: 200.1-600 m/z
-Peaks: 15230 (about 3808 per sample)
-Peak Groups: 6332 
+Peaks: 15405 (about 3851 per sample)
+Peak Groups: 6349 
 Sample classes: KO, WT 
 
 Feature detection:
@@ -136,7 +137,7 @@
 Profile settings: method = bin
                   step = 0.1
 
-Memory usage: 3.11 MB
+Memory usage: 3.98 MB
 </pre></div>
 <h2>Citations:</h2>
 <div><ul>
diff -r acc66e5c23d7 -r db6549f27ad1 test-data/faahKO.xset.group.retcor.group.fillpeaks.RData
Binary file test-data/faahKO.xset.group.retcor.group.fillpeaks.RData has changed
diff -r acc66e5c23d7 -r db6549f27ad1 test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html
--- a/test-data/faahKO.xset.group.retcor.group.fillpeaks.summary.html	Wed Feb 12 08:30:41 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-<!DOCTYPE html>
-<HTML lang='en'>
-<HEAD>
-<meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
-<title>[W4M] XCMS analysis summary</title>
-<style>
-table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }
-td,th { padding: 5px; padding-right: 12px; }
-th { background: #898989; text-align:left;color: white;}
-h2 { color: #FFA212; }
-ul li { margin-bottom:10px; }
-</style>
-</HEAD>
-<BODY>
-<div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
-</div>
-<h2>Samples used:</h2>
-<div><table>
-<tr><th>sample</th><th>filename</th><th>md5sum<sup>*</sup></th></tr>
-<tr><td>ko15</td><td>faahKO_reduce/KO/ko15.CDF</td><td>4698c36c0b3af007faf70975c04ccf2a</td></tr><tr><td>ko16</td><td>faahKO_reduce/KO/ko16.CDF</td><td>afaeed94ced3140bc042d5ab6aeb16c1</td></tr><tr><td>wt15</td><td>faahKO_reduce/WT/wt15.CDF</td><td>d58a27fad7c04ddddb0359ddc2b7ba68</td></tr><tr><td>wt16</td><td>faahKO_reduce/WT/wt16.CDF</td><td>29654e9f8ad48c1fbe2a41b9ba578f6e</td></tr>
-</table>
-<br/><sup>*</sup>The program md5sum is designed to verify data integrity. So you can check if the data were uploaded correctly or if the data were changed during the process.
-</div>
-<h2>Function launched:</h2>
-<div><table>
-<tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
-<tr><td rowspan='4'>160420-14:09:46</td><td rowspan='4'>xcmsSet</td>
-<td>nSlaves</td><td>1</td></tr>
-<tr><td>method</td><td>centWave</td></tr>
-<tr><td>ppm</td><td>25</td></tr>
-<tr><td>peakwidth</td><td>2050</td></tr>
-<tr><td rowspan='6'>160420-15:07:14</td><td rowspan='6'>group</td>
-<td>method</td><td>density</td></tr>
-<tr><td>sleep</td><td>0.001</td></tr>
-<tr><td>minfrac</td><td>0.3</td></tr>
-<tr><td>bw</td><td>5</td></tr>
-<tr><td>mzwid</td><td>0.01</td></tr>
-<tr><td>max</td><td>50</td></tr>
-<tr><td rowspan='7'>160421-11:10:32</td><td rowspan='7'>retcor</td>
-<td>method</td><td>peakgroups</td></tr>
-<tr><td>smooth</td><td>loess</td></tr>
-<tr><td>extra</td><td>1</td></tr>
-<tr><td>missing</td><td>1</td></tr>
-<tr><td>span</td><td>0.2</td></tr>
-<tr><td>family</td><td>gaussian</td></tr>
-<tr><td>plottype</td><td>deviation</td></tr>
-<tr><td rowspan='6'>160421-11:19:31</td><td rowspan='6'>group</td>
-<td>method</td><td>density</td></tr>
-<tr><td>sleep</td><td>0.001</td></tr>
-<tr><td>minfrac</td><td>0.3</td></tr>
-<tr><td>bw</td><td>5</td></tr>
-<tr><td>mzwid</td><td>0.01</td></tr>
-<tr><td>max</td><td>50</td></tr>
-<tr><td rowspan='1'>160421-11:50:48</td><td rowspan='1'>fillPeaks</td>
-<td>method</td><td>chrom</td></tr>
-</table>
-<br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss
-</div>
-<h2>Informations about the xcmsSet object:</h2>
-<div><pre>
-An "xcmsSet" object with 4 samples
-
-Time range: 2506-4484 seconds (41.8-74.7 minutes)
-Mass range: 200.1-600 m/z
-Peaks: 32720 (about 8180 per sample)
-Peak Groups: 8157 
-Sample classes: KO, WT 
-
-Feature detection:
-Profile settings: method = bin
-                  step = 0.1
-
-Memory usage: 4.25 MB
-</pre></div>
-<h2>Citations:</h2>
-<div><ul>
-<li>To cite the <b>XCMS</b> package in publications use:
-<ul>
-<li>Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)</li>
-<li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
-<li>H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)</li>
-</ul>
-</li>
-<li>To cite the <b>CAMERA</b> package in publications use:
-<ul>
-<li>Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)</li>
-</ul>
-</li>
-<li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
-<ul>
-<li>Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics  doi:10.1093/bioinformatics/btu813</li>
-</ul>
-</li>
-</ul></div>
-</BODY>
-</HTML>
diff -r acc66e5c23d7 -r db6549f27ad1 xcms_summary.r
--- a/xcms_summary.r	Wed Feb 12 08:30:41 2020 -0500
+++ b/xcms_summary.r	Tue May 12 16:39:28 2020 -0400
@@ -67,18 +67,22 @@
 if (!is.null(args$user_email)) user_email = args$user_email;
 
 # if the RData come from XCMS 1.x
-if (exists("xset")) xobject <- xset
-# retrocompatability
-if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))
+if (exists("xset")) {
+    xobject <- xset
+    # retrocompatability
+    if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(sampnames(xobject)))
+}
 # if the RData come from CAMERA
 if (exists("xa")) xobject <- xa@xcmsSet
 # if the RData come from XCMS 3.x
-if (exists("xdata")) xobject <- xdata
+if (exists("xdata")) {
+    xobject <- xdata
+    if (!exists("sampleNamesList")) sampleNamesList <- list("sampleNamesMakeNames"=make.names(xdata@phenoData@data$sample_name))
+}
 
 if (!exists("xobject")) stop("You need at least a xdata, a xset or a xa object.")
 
 
-
 # ----- MAIN PROCESSING INFO -----
 writehtml("<!DOCTYPE html>")
 writehtml("<HTML lang='en'>")