# HG changeset patch
# User lecorguille
# Date 1549038575 18000
# Node ID b6a8143c397c526eb0817705ed60fe5f44773bcc
# Parent  b02797fbead14b88ba6ad038d71f9e119b43215c
planemo upload commit aa538ae477bc2f901c95d916e11d70eab75b5e00

diff -r b02797fbead1 -r b6a8143c397c CAMERA.r
--- a/CAMERA.r	Fri Aug 17 06:45:55 2018 -0400
+++ b/CAMERA.r	Fri Feb 01 11:29:35 2019 -0500
@@ -83,11 +83,6 @@
     rplotspdf = listArguments[["rplotspdf"]]; listArguments[["rplotspdf"]]=NULL
 }
 
-dataMatrixOutput = "dataMatrix.tsv"
-if (!is.null(listArguments[["dataMatrixOutput"]])){
-    dataMatrixOutput = listArguments[["dataMatrixOutput"]]; listArguments[["dataMatrixOutput"]]=NULL
-}
-
 variableMetadataOutput = "variableMetadata.tsv"
 if (!is.null(listArguments[["variableMetadataOutput"]])){
     variableMetadataOutput = listArguments[["variableMetadataOutput"]]; listArguments[["variableMetadataOutput"]]=NULL
@@ -129,7 +124,7 @@
 pdf(file=rplotspdf, width=16, height=12)
 
 if (thefunction %in% c("annotatediff")) {
-    results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput)
+    results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput)
     xa=results_list[["xa"]]
     diffrep=results_list[["diffrep"]]
     variableMetadata=results_list[["variableMetadata"]]
diff -r b02797fbead1 -r b6a8143c397c README.rst
--- a/README.rst	Fri Aug 17 06:45:55 2018 -0400
+++ b/README.rst	Fri Feb 01 11:29:35 2019 -0500
@@ -2,6 +2,14 @@
 Changelog/News
 --------------
 
+**Version 2.2.5 - 01/02/2019**
+
+- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
+
+**Version 2.2.4 - 09/10/2018**
+
+- NES: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
+
 **Version 2.2.3 - 30/04/2018**
 
 - NEW: support the new xcms 3.0.0 wrapper
diff -r b02797fbead1 -r b6a8143c397c abims_CAMERA_annotateDiffreport.xml
--- a/abims_CAMERA_annotateDiffreport.xml	Fri Aug 17 06:45:55 2018 -0400
+++ b/abims_CAMERA_annotateDiffreport.xml	Fri Feb 01 11:29:35 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.3">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.5">
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
 
@@ -18,7 +18,6 @@
 
         ## output
         variableMetadataOutput '$variableMetadata'
-        dataMatrixOutput '$datamatrix'
 
         ## groupFWHM
         sigma $groupfwhm.sigma
@@ -67,6 +66,8 @@
             h $diffreport.options.h
             w $diffreport.options.w
             mzdec $diffreport.options.mzdec
+            tabular2 $diffreport.options.tabular2
+            png2 $diffreport.options.png2
         #end if
 
         @COMMAND_PEAKLIST@
@@ -160,6 +161,14 @@
                     <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" />
                     <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" />
                     <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/>
+                    <param name="tabular2" type="select" label="Export the Diffreport files in ">
+                        <option value="zip" selected="true">Zip</option>
+                        <option value="datasetcollection">Individual file in a Dataset Collection</option>
+                    </param>
+                    <param name="png2" type="select" label="Export the EIC and boxplots in ">
+                        <option value="zip" selected="true">Zip</option>
+                        <option value="pdf">Individual pdf</option>
+                    </param>
                 </when>
                 <when value="hide">
                 </when>
@@ -172,7 +181,6 @@
 
     <outputs>
         <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" />
-        <data name="datamatrix" format="tabular" label="${image.name[:-6]}.annotate.dataMatrix.tsv" />
         <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" >
             <filter>quick_block['quick'] == 'FALSE'</filter>
             <change_format>
@@ -183,11 +191,25 @@
         <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" >
             <filter>quick_block['quick'] == 'TRUE'</filter>
         </data>
-        <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="true">
-            <filter>diffreport['options']['option'] == 'show'</filter>
-            <discover_datasets pattern="__designation_and_ext__" directory="pdf" visible="true" />
-            <discover_datasets pattern="__designation_and_ext__" directory="tabular" visible="true" />
+
+        <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip" >
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter>
+        </data>
+        <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip" >
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'zip'</filter>
         </data>
+        <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf">
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['png2'] == 'pdf'</filter>
+            <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" visible="true" />
+        </collection>
+
+        <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport.pdf" from_work_dir="tabular.zip">
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter>
+        </data>
+        <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table">
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter>
+            <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" visible="true" />
+        </collection>
     </outputs>
 
     <tests>
@@ -197,23 +219,20 @@
             <expand macro="test_annotate_quick_true"/>
             <expand macro="test_file_load_zip"/>
             <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
-            <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
         </test>-->
         <test>
             <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
             <expand macro="test_annotate_diffreport"/>
             <expand macro="test_annotate_quick_true"/>
             <expand macro="test_file_load_single"/>
-            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
-            <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
+            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" lines_diff="2" />
         </test>
         <test>
             <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData"/>
             <expand macro="test_annotate_diffreport"/>
             <expand macro="test_annotate_quick_true"/>
             <expand macro="test_file_load_single"/>
-            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv" />
-            <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix-xcms3.tsv" />
+            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata-xcms3.tsv" lines_diff="2" />
         </test>
         <test>
             <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData"/>
@@ -229,8 +248,7 @@
                 </section>
             </conditional>
             <expand macro="test_file_load_single"/>
-            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" />
-            <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.dataMatrix.tsv" />
+            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" lines_diff="2"/>
         </test>
     </tests>
 
@@ -287,19 +305,19 @@
 +===========================+=======================================+================================================+
 |CAMERA_combinexsAnnot      |xset.annotate.Rdata                    | rdata.camera.positive or rdata.camera.negative |
 +---------------------------+---------------------------------------+------------------------------------------------+
-|Determine Vdk or Lowess    |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+|Determine Vdk or Lowess    |xset.annotate.variableMetadata.tsv     | Tabular                                        |
 +---------------------------+---------------------------------------+------------------------------------------------+
-|Normalization Vdk/Lowess   |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+|Normalization Vdk/Lowess   |xset.annotate.variableMetadata.tsv     | Tabular                                        |
 +---------------------------+---------------------------------------+------------------------------------------------+
-|Anova                      |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+|Anova                      |xset.annotate.variableMetadata.tsv     | Tabular                                        |
 +---------------------------+---------------------------------------+------------------------------------------------+
-|PCA                        |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+|PCA                        |xset.annotate.variableMetadata.tsv     | Tabular                                        |
 +---------------------------+---------------------------------------+------------------------------------------------+
-|Hierarchical Clustering    |xset.annotate.dataMatrix.tsv           | Tabular                                        |
+|Hierarchical Clustering    |xset.annotate.variableMetadata.tsv     | Tabular                                        |
 +---------------------------+---------------------------------------+------------------------------------------------+
 
 
-The output file **xset.annotate.dataMatrix.tsv** is an tabular file. You can continue your analysis using it in the following tools:
+The output file **xset.annotate.variableMetadata.tsv** is an tabular file. You can continue your analysis using it in the following tools:
 
     | Determine Vdk or Lowess
     | Normalization Vdk/Lowess
@@ -361,10 +379,6 @@
     | For each metabolite (row) :
     | the value of the intensity in each sample, fold, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct and pcgroup
 
-xset.annotate.dataMatrix.tsv
-
-    | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column).
-
 xset.annotate.zip
 
     | It contains filebase_eic, filebase_box and filebase.tsv for one conditon vs another (Anova analysis).
@@ -377,7 +391,7 @@
 
 .. class:: infomark
 
-The output **"xset.annotate.dataMatrix.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow:
+The output **"xset.annotate.variableMetadata.tsv"** is a tabular file. You can continue your analysis using it in the following tools of the workflow:
 
     | Determine Vdk or Lowess (Data correction)
     | Normalization Vdk/Lowess (Data correction)
@@ -418,10 +432,6 @@
 Output files
 ------------
 
-**Example of an xset.annotate.dataMatrix.tsv output**
-
-.. image:: annotatediffreport_dataMatrix.png
-
 **Example of a part of xset.annotate.variableMetadata.tsv output**
 
 .. image:: annotatediffreport_variableMetadata.png
@@ -432,6 +442,14 @@
 Changelog/News
 --------------
 
+**Version 2.2.5 - 01/02/2019**
+
+- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
+
+**Version 2.2.4 - 09/10/2018**
+
+- NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
+
 **Version 2.2.3 - 30/04/2018**
 
 - NEW: support the new xcms 3.0.0 wrapper
diff -r b02797fbead1 -r b6a8143c397c lib.r
--- a/lib.r	Fri Aug 17 06:45:55 2018 -0400
+++ b/lib.r	Fri Feb 01 11:29:35 2019 -0500
@@ -34,6 +34,18 @@
 }
 
 #@author G. Le Corguille
+#The function create a zip archive from the different png generated by diffreport
+diffreport_png2zip <- function() {
+    zip("eic.zip",dir(pattern="_eic"))
+    zip("box.zip",dir(pattern="_box"))
+}
+
+#The function create a zip archive from the different tabular generated by diffreport
+diffreport_tabular2zip <- function() {
+    zip("tabular.zip",dir(pattern="tabular/*"))
+}
+
+#@author G. Le Corguille
 #This function convert if it is required the Retention Time in minutes
 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
     if (convertRTMinute){
@@ -57,7 +69,7 @@
 }
 
 #The function annotateDiffreport without the corr function which bugs
-annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv") {
+annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv") {
     # Resolve the bug with x11, with the function png
     options(bitmapType='cairo')
 
@@ -108,11 +120,6 @@
     peakList=getPeaklist(xa,intval=listArguments[["intval"]])
     peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
 
-    # --- dataMatrix ---
-    dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c("name", make.names(sampnames(xa@xcmsSet))))]
-    write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput)
-
-
     # --- Multi condition : diffreport ---
     diffrepOri=NULL
     if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
@@ -149,11 +156,16 @@
                     write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))
 
                     if (listArguments[["eicmax"]] != 0) {
-                        diffreport_png2pdf(filebase)
+                        if (listArguments[["png2"]] == "pdf")
+                            diffreport_png2pdf(filebase)
                     }
                 }
             }
         }
+        if (listArguments[["png2"]] == "zip")
+            diffreport_png2zip()
+        if (listArguments[["tabular2"]] == "zip")
+            diffreport_tabular2zip()
     }
 
     # --- variableMetadata ---
@@ -330,24 +342,24 @@
 getEIC <- function(object, mzrange, rtrange = 200,
                    groupidx, sampleidx = sampnames(object),
                    rt = c("corrected", "raw")) {
-    
+
     files <- filepaths(object)
     grp <- groups(object)
     samp <- sampnames(object)
     prof <- profinfo(object)
-    
+
     rt <- match.arg(rt)
-    
+
     if (is.numeric(sampleidx))
     sampleidx <- sampnames(object)[sampleidx]
     sampidx <- match(sampleidx, sampnames(object))
-    
+
     if (!missing(groupidx)) {
         if (is.numeric(groupidx))
         groupidx <- groupnames(object)[unique(as.integer(groupidx))]
         grpidx <- match(groupidx, groupnames(object, template = groupidx))
     }
-    
+
     if (missing(mzrange)) {
         if (missing(groupidx))
         stop("No m/z range or groups specified")
@@ -369,7 +381,7 @@
     else if (is.null(dim(mzrange)))
     stop("mzrange must be a matrix")
     colnames(mzrange) <- c("mzmin", "mzmax")
-    
+
     if (length(rtrange) == 1) {
         if (missing(groupidx))
         rtrange <- matrix(rep(range(object@rt[[rt]][sampidx]), nrow(mzrange)),
@@ -380,11 +392,11 @@
     } else if (is.null(dim(rtrange)))
     stop("rtrange must be a matrix or single number")
     colnames(rtrange) <- c("rtmin", "rtmax")
-    
+
     ## Ensure that we've got corrected retention time if requested.
     if (is.null(object@rt[[rt]]))
     stop(rt, " retention times not present in 'object'!")
-    
+
     ## Ensure that the defined retention time range is within the rtrange of the
     ## object: we're using the max minimal rt of all files and the min maximal rt
     rtrs <- lapply(object@rt[[rt]], range)
@@ -406,17 +418,17 @@
         rtrange[lower_rt_outside, "rtmin"] <- rtr[1]
         rtrange[upper_rt_outside, "rtmax"] <- rtr[2]
     }
-    
+
     if (missing(groupidx))
     gnames <- character(0)
     else
     gnames <- groupidx
-    
+
     eic <- vector("list", length(sampleidx))
     names(eic) <- sampleidx
-    
+
     for (i in seq(along = sampidx)) {
-        
+
         ## cat(sampleidx[i], "")
         flush.console()
         ## getXcmsRaw takes care of rt correction, susetting to scanrage and other
@@ -428,7 +440,7 @@
         gc()
     }
     ## cat("\n")
-    
+
     invisible(new("xcmsEIC", eic = eic, mzrange = mzrange, rtrange = rtrange,
     rt = rt, groupnames = gnames))
 }
@@ -449,15 +461,15 @@
                       metlin = FALSE,
                       h = 480, w = 640, mzdec=2,
                       missing = numeric(), ...) {
-    
+
     if ( nrow(object@groups)<1 || length(object@groupidx) <1) {
         stop("No group information. Use group().")
     }
-    
+
     if (!is.numeric(w) || !is.numeric(h))
         stop("'h' and 'w' have to be numeric")
     ## require(multtest) || stop("Couldn't load multtest")
-    
+
     value <- match.arg(value)
     groupmat <- groups(object)
     if (length(groupmat) == 0)
@@ -466,20 +478,20 @@
     n <- length(samples)
     classlabel <- sampclass(object)
     classlabel <- levels(classlabel)[as.vector(unclass(classlabel))]
-    
+
     values <- groupval(object, "medret", value=value)
     indecies <- groupval(object, "medret", value = "index")
-    
+
     if (!all(c(class1,class2) %in% classlabel))
     stop("Incorrect Class Labels")
-    
+
     ## c1 and c2 are column indices of class1 and class2 resp.
     c1 <- which(classlabel %in% class1)
     c2 <- which(classlabel %in% class2)
     ceic <- which(classlabel %in% classeic)
     if (length(intersect(c1, c2)) > 0)
     stop("Intersecting Classes")
-    
+
     ## Optionally replace NA values with the value provided with missing
     if (length(missing)) {
         if (is.numeric(missing)) {
@@ -493,21 +505,21 @@
     warning("`NA` values in xcmsSet. Use fillPeaks() on the object to fill",
     "-in missing peak values. Note however that this will also ",
     "insert intensities of 0 for peaks that can not be filled in.")
-    
+
     mean1 <- rowMeans(values[,c1,drop=FALSE], na.rm = TRUE)
     mean2 <- rowMeans(values[,c2,drop=FALSE], na.rm = TRUE)
-    
+
     ## Calculate fold change.
     ## For foldchange <1 set fold to 1/fold
     ## See tstat to check which was higher
     fold <- mean2 / mean1
     fold[!is.na(fold) & fold < 1] <- 1/fold[!is.na(fold) & fold < 1]
-    
+
     testval <- values[,c(c1,c2)]
     ## Replace eventual infinite values with NA (CAMERA issue #33)
     testval[is.infinite(testval)] <- NA
     testclab <- c(rep(0,length(c1)),rep(1,length(c2)))
-    
+
     if (min(length(c1), length(c2)) >= 2) {
         tstat <- mt.teststat(testval, testclab, ...)
         pvalue <- xcms:::pval(testval, testclab, tstat)
@@ -543,18 +555,18 @@
         values<-values[tsidx,]
     } else
     tsidx <- 1:nrow(values)
-    
+
     if (length(filebase))
     write.table(twosamp, paste(filebase, ".tsv", sep = ""), quote = FALSE, sep = "\t", col.names = NA)
-    
+
     if (eicmax > 0) {
         if (length(unique(peaks(object)[,"rt"])) > 1) {
             ## This looks like "normal" LC data
-            
+
             eicmax <- min(eicmax, length(tsidx))
             eics <- getEIC(object, rtrange = eicwidth*1.1, sampleidx = ceic,
             groupidx = tsidx[seq(length = eicmax)])
-            
+
             if (length(filebase)) {
                 eicdir <- paste(filebase, "_eic", sep="")
                 boxdir <- paste(filebase, "_box", sep="")
@@ -572,7 +584,7 @@
                 }
             }
             plot(eics, object, rtrange = eicwidth, mzdec=mzdec)
-            
+
             if (length(filebase))
             dev.off()
         } else {
@@ -596,13 +608,13 @@
                     height = h/72, onefile = FALSE)
                 }
             }
-            
+
             plotSpecWindow(object, gidxs = tsidx[seq(length = eicmax)], borderwidth=1)
-            
+
             if (length(filebase))
             dev.off()
         }
     }
-    
+
     invisible(twosamp)
 }
diff -r b02797fbead1 -r b6a8143c397c repository_dependencies.xml
--- a/repository_dependencies.xml	Fri Aug 17 06:45:55 2018 -0400
+++ b/repository_dependencies.xml	Fri Feb 01 11:29:35 2019 -0500
@@ -1,5 +1,5 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories>
-	<repository changeset_revision="3319a4f78021" name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-	<repository changeset_revision="8ce71291b600" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository changeset_revision="3319a4f78021" name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="8ce71291b600" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+</repositories>
\ No newline at end of file