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changeset 9:c02d80efba80 draft

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planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
author lecorguille
date Sun, 10 Apr 2016 08:14:59 -0400
parents 821f2d271ea8
children 01a900f2e464
files CAMERA.r abims_CAMERA_annotateDiffreport.xml lib.r macros.xml planemo.sh tool_dependencies.xml
diffstat 6 files changed, 405 insertions(+), 57 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CAMERA.r	Sun Apr 10 08:14:59 2016 -0400
@@ -0,0 +1,146 @@
+#!/usr/bin/env Rscript
+# CAMERA.r version="2.2.1"
+
+
+
+# ----- PACKAGE -----
+cat("\tPACKAGE INFO\n")
+
+#pkgs=c("xcms","batch")
+pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "tcltk","igraph", "xcms","snow","CAMERA","multtest","batch")
+for(p in pkgs) {
+  suppressPackageStartupMessages(suppressWarnings(library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
+  cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
+}
+source_local <- function(fname){ argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
+
+cat("\n\n"); 
+
+
+
+# ----- ARGUMENTS -----
+cat("\tARGUMENTS INFO\n")
+
+listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
+write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
+
+cat("\n\n");
+
+
+# ----- PROCESSING INFILE -----
+cat("\tINFILE PROCESSING INFO\n")
+
+#image is an .RData file necessary to use xset variable given by previous tools
+if (!is.null(listArguments[["image"]])){
+  load(listArguments[["image"]]); listArguments[["image"]]=NULL
+}
+
+if (listArguments[["xfunction"]] %in% c("combinexsAnnos")) {
+  load(listArguments[["image_pos"]])
+  xaP=xa  
+  if (exists("xsAnnotate_object")) xaP=xsAnnotate_object
+  
+  diffrepP=NULL
+  if (exists("diffrep")) diffrepP=diffrep
+
+  load(listArguments[["image_neg"]])
+  xaN=xa
+  if (exists("xsAnnotate_object")) xaN=xsAnnotate_object
+
+  diffrepN=NULL
+  if (exists("diffrep")) diffrepN=diffrep
+}
+
+
+cat("\n\n")
+
+
+# ----- ARGUMENTS PROCESSING -----
+cat("\tARGUMENTS PROCESSING INFO\n")
+
+# Save arguments to generate a report
+if (!exists("listOFlistArguments")) listOFlistArguments=list()
+listOFlistArguments[[paste(format(Sys.time(), "%y%m%d-%H:%M:%S_"),listArguments[["xfunction"]],sep="")]] = listArguments
+
+
+#saving the commun parameters
+thefunction = listArguments[["xfunction"]]
+listArguments[["xfunction"]]=NULL #delete from the list of arguments
+
+xsetRdataOutput = paste(thefunction,"RData",sep=".")
+if (!is.null(listArguments[["xsetRdataOutput"]])){
+  xsetRdataOutput = listArguments[["xsetRdataOutput"]]; listArguments[["xsetRdataOutput"]]=NULL
+}
+
+rplotspdf = "Rplots.pdf"
+if (!is.null(listArguments[["rplotspdf"]])){
+  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
+}
+
+if (!is.null(listArguments[["new_file_path"]])){
+  new_file_path = listArguments[["new_file_path"]]; listArguments[["new_file_path"]]=NULL
+}
+
+#Import the different functions
+source_local("lib.r")
+
+# We unzip automatically the chromatograms from the zip files.
+if (thefunction == "annotatediff")  {
+  if(exists("zipfile") && (zipfile!="")) {
+    suppressWarnings(unzip(zipfile, unzip="unzip"))
+  }
+}
+
+
+#addition of xset object to the list of arguments in the first position
+if (exists("xset") != 0){
+  listArguments=append(list(xset), listArguments)
+}
+
+cat("\n\n")
+
+
+
+
+# ----- PROCESSING INFO -----
+cat("\tMAIN PROCESSING INFO\n")
+
+#change the default display settings
+pdf(file=rplotspdf, width=16, height=12)
+
+
+if (thefunction %in% c("annotatediff")) {
+  results_list=annotatediff(xset=xset,listArguments=listArguments,variableMetadataOutput=variableMetadataOutput,dataMatrixOutput=dataMatrixOutput,new_file_path=new_file_path)
+  xa=results_list[["xa"]]
+  diffrep=results_list[["diffrep"]]
+  variableMetadata=results_list[["variableMetadata"]]
+
+  cat("\n\n")
+  cat("\tXSET OBJECT INFO\n")
+  print(xa)
+}
+
+if (thefunction %in% c("combinexsAnnos")) {
+  cAnnot=combinexsAnnos_function(xaP=xaP,xaN=xaN,diffrepP=diffrepP,diffrepN=diffrepN,convert_param=listArguments[["convert_param"]],pos=listArguments[["pos"]],tol=listArguments[["tol"]],ruleset=listArguments[["ruleset"]],keep_meta=listArguments[["keep_meta"]],variableMetadataOutput=variableMetadataOutput)
+}
+
+dev.off()
+
+
+#saving R data in .Rdata file to save the variables used in the present tool
+objects2save = c("xa","variableMetadata","diffrep","cAnnot","listOFlistArguments","zipfile")
+save(list=objects2save[objects2save %in% ls()], file=xsetRdataOutput)
+
+cat("\n\n")
+
+cat("\tDONE\n")
--- a/abims_CAMERA_annotateDiffreport.xml	Mon Feb 22 17:09:43 2016 -0500
+++ b/abims_CAMERA_annotateDiffreport.xml	Sun Apr 10 08:14:59 2016 -0400
@@ -2,23 +2,15 @@
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
     
-    <requirements>
-        <requirement type="package" version="3.1.2">R</requirement>
-        <requirement type="binary">Rscript</requirement>
-        <requirement type="package" version="1.44.0">xcms</requirement>
-        <requirement type="package" version="1.22.0">camera</requirement>
-        <requirement type="package" version="2.2.1">camera_w4m_script</requirement>
-        <requirement type="binary">CAMERA.r</requirement>
-        <requirement type="package" version="1.3.18">graphicsmagick</requirement>
-        <requirement type="binary">convert</requirement>
-    </requirements>
-    
-    <stdio>
-        <exit_code range="1:" level="fatal" />
-    </stdio>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
     <command><![CDATA[
-        CAMERA.r 
+        @COMMAND_CAMERA_SCRIPT@
         xfunction annotatediff 
         image $image
 
@@ -162,26 +154,25 @@
             <param name="mzabs" value="0.015"/>
             <param name="intval" value="into"/>
             <param name="max_peaks" value="100"/>
-            <param name="quick_block.quick" value="FALSE"/>
-            <param name="quick_block.polarity" value="negative"/>
-            <param name="quick_block.cor_eic_th" value="0.75"/>
-            <param name="quick_block.graphMethod" value="hcs"/>
-            <param name="quick_block.pval" value="0.05"/>
-            <param name="quick_block.calcCiS" value="True"/>
-            <param name="quick_block.calcIso" value="False"/>
-            <param name="quick_block.calcCaS" value="False"/>
-            <param name="quick_block.multiplier" value="3"/>
-            <param name="options.option" value="show"/>
-            <param name="options.eicmax" value="200"/>
-            <param name="options.eicwidth" value="200"/>
-            <param name="options.value" value="into"/>
-            <param name="options.h" value="480"/>
-            <param name="options.w" value="640"/>
-            <param name="options.mzdec" value="2"/>
-            <param name="options.sortpval" value="False"/>
+            <param name="quick_block|quick" value="FALSE"/>
+            <param name="quick_block|polarity" value="negative"/>
+            <param name="quick_block|cor_eic_th" value="0.75"/>
+            <param name="quick_block|graphMethod" value="hcs"/>
+            <param name="quick_block|pval" value="0.05"/>
+            <param name="quick_block|calcCiS" value="True"/>
+            <param name="quick_block|calcIso" value="False"/>
+            <param name="quick_block|calcCaS" value="False"/>
+            <param name="quick_block|multiplier" value="3"/>
+            <param name="options|option" value="show"/>
+            <param name="options|eicmax" value="200"/>
+            <param name="options|eicwidth" value="200"/>
+            <param name="options|value" value="into"/>
+            <param name="options|h" value="480"/>
+            <param name="options|w" value="640"/>
+            <param name="options|mzdec" value="2"/>
+            <param name="options|sortpval" value="False"/>
             <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" />
             <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" />
-            <output name="rdata" file="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" />
         </test>
     </tests>
     
@@ -189,18 +180,7 @@
     
     <help><![CDATA[
         
-.. class:: infomark
-
-**Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de
-
-.. class:: infomark
-
-**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
-
- | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
-
----------------------------------------------------
-
+@HELP_AUTHORS@
 
 ================
 CAMERA.annotate
@@ -405,10 +385,7 @@
 
     ]]></help>
 
-    <citations>
-        <citation type="doi">10.1021/ac202450g</citation>
-        <citation type="doi">10.1093/bioinformatics/btu813</citation>
-    </citations>
+    <expand macro="citation" />
 
 
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib.r	Sun Apr 10 08:14:59 2016 -0400
@@ -0,0 +1,185 @@
+# lib.r version="2.2.1"
+
+#The function create a pdf from the different png generated by diffreport
+diffreport_png2pdf <- function(filebase, new_file_path) {
+
+  pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="")
+  pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="")
+
+  system(paste("convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep=""))
+  system(paste("convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep=""))
+
+  file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput)
+  file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput)
+}
+
+#The function annotateDiffreport without the corr function which bugs
+annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) {
+  # Resolve the bug with x11, with the function png
+  options(bitmapType='cairo')
+
+  #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
+  res=try(is.null(xset@filled))
+
+  # ------ annot -------
+  listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])
+  listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])
+  listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])
+
+  #graphMethod parameter bugs where this parameter is not defined in quick=true
+  if(listArguments[["quick"]]==TRUE) {
+    xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
+  }
+  else {
+    xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]],multiplier=listArguments[["multiplier"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
+
+  }  
+  peakList=getPeaklist(xa,intval=listArguments[["intval"]])
+  peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
+
+
+  # --- Multi condition : diffreport --- 
+  diffrep=NULL
+  if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
+    #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
+    res=try(is.null(xset@filled))
+    classes=levels(sampclass(xset))
+    x=1:(length(classes)-1)
+    for (i in seq(along=x) ) {
+      y=1:(length(classes))
+      for (n in seq(along=y)){
+        if(i+n <= length(classes)){
+          filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
+
+          diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]])
+          #combines results
+          diffreportTSV=merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
+          diffreportTSV=cbind(diffreportTSV[,!(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))],diffreportTSV[,(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))])
+
+          if(listArguments[["sortpval"]]){
+            diffreportTSV=diffreportTSV[order(diffreportTSV$pvalue), ]
+          }
+    
+          if (listArguments[["convert_param"]]){
+              #converting the retention times (seconds) into minutes
+              diffreportTSV$rt=diffreportTSV$rt/60;diffreportTSV$rtmin=diffreportTSV$rtmin/60; diffreportTSV$rtmax=diffreportTSV$rtmax/60;
+          }
+          write.table(diffreportTSV, sep="\t", quote=FALSE, row.names=FALSE, file=paste(new_file_path,filebase,"-tabular_visible_tabular",sep=""))
+
+          if (listArguments[["eicmax"]] != 0) {
+              diffreport_png2pdf(filebase, new_file_path)
+          }
+        }
+      }
+    }
+  }
+
+
+
+
+  # --- variableMetadata ---
+  variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
+  # if we have 2 conditions, we keep stat of diffrep
+  if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) {
+    variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
+    if(exists("listArguments[[\"sortpval\"]]")){
+      variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
+    }
+  }
+
+  variableMetadataOri=variableMetadata
+  if (listArguments[["convert_param"]]){
+    #converting the retention times (seconds) into minutes
+    print("converting the retention times into minutes in the variableMetadata")
+    variableMetadata$rt=variableMetadata$rt/60;variableMetadata$rtmin=variableMetadata$rtmin/60; variableMetadata$rtmax=variableMetadata$rtmax/60;
+  }
+  #Transform metabolites name
+  variableMetadata$name= paste("M",round(variableMetadata$mz,digits=listArguments[["num_digits"]]),"T",round(variableMetadata$rt),sep="")    
+  write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
+
+  # --- dataMatrix ---
+  dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
+  dataMatrix=cbind(peakList$name,dataMatrix); colnames(dataMatrix)[1] = c("name");
+
+  if (listArguments[["convert_param"]]){
+    #converting the retention times (seconds) into minutes
+    print("converting the retention times into minutes in the dataMatrix ids")
+    peakList$rt=peakList$rt/60
+  }
+  dataMatrix$name= paste("M",round(peakList$mz,digits=listArguments[["num_digits"]]),"T",round(peakList$rt),sep="")
+  write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput)
+  
+  return(list("xa"=xa,"diffrep"=diffrep,"variableMetadata"=variableMetadataOri));
+
+}
+
+
+combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){
+
+  #Load the two Rdata to extract the xset objects from positive and negative mode
+  cat("\tObject xset from positive mode\n")
+  print(xaP)
+  cat("\n")  
+
+  cat("\tObject xset from negative mode\n")
+  print(xaN)
+  cat("\n")
+    
+  cat("\n")
+  cat("\tCombining...\n")
+  #Convert the string to numeric for creating matrix
+  row=as.numeric(strsplit(ruleset,",")[[1]][1])
+  column=as.numeric(strsplit(ruleset,",")[[1]][2])
+  ruleset=cbind(row,column)
+  #Test if the file comes from an older version tool
+  if ((!is.null(xaP)) & (!is.null(xaN))) {
+    #Launch the combinexsannos function from CAMERA
+    cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)
+  } else {
+    stop("You must relauch the CAMERA.annotate step with the lastest version.")
+  }
+
+  
+
+  if(pos){
+    xa=xaP
+    mode="neg. Mode"
+  } else {
+    xa=xaN
+    mode="pos. Mode"
+  }
+  peakList=getPeaklist(xa,intval=listArguments[["intval"]])
+  peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
+  variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
+  variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
+
+  #Test if there are more than two classes (conditions)
+  if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
+    diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")
+    diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")
+    
+    variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")
+    variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")
+  } 
+    
+  rownames(variableMetadata) = NULL
+  #TODO: checker
+  #colnames(variableMetadata)[1:2] = c("name","mz/rt");
+
+  #If the user want to convert the retention times (seconds) into minutes.
+  if (listArguments[["convert_param"]]){
+    #converting the retention times (seconds) into minutes
+    cat("\tConverting the retention times into minutes\n")
+    variableMetadata$rtmed=cAnnot$rt/60; variableMetadata$rtmin=cAnnot$rtmin/60; variableMetadata$rtmax=cAnnot$rtmax/60;
+  }
+
+  #If the user want to keep only the metabolites which match a difference
+  if(keep_meta){
+    variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]
+  }
+      
+  #Write the output into a tsv file
+  write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
+  return(variableMetadata);
+
+}
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sun Apr 10 08:14:59 2016 -0400
@@ -0,0 +1,44 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.1.2">R</requirement>
+	    <requirement type="package" version="0.4_1">r-snow</requirement>
+            <requirement type="package" version="1.44.0">bioconductor-camera</requirement>
+	    <requirement type="package" version="1.1_4">r-batch</requirement>
+            <requirement type="package" version="1.3.20">graphicsmagick</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1" level="fatal" />
+        </stdio>
+    </xml>
+
+    <token name="@COMMAND_CAMERA_SCRIPT@">
+        LANG=C Rscript $__tool_directory__/CAMERA.r
+    </token>
+
+    <token name="@HELP_AUTHORS@">
+.. class:: infomark
+
+**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu 
+
+.. class:: infomark
+
+**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
+
+ | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
+
+---------------------------------------------------
+
+    </token>
+
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1021/ac202450g</citation>
+            <citation type="doi">10.1093/bioinformatics/btu813</citation>
+        </citations>
+    </xml>
+</macros>
--- a/planemo.sh	Mon Feb 22 17:09:43 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-planemo shed_init -f --name=camera_annotate --owner=lecorguille --description="[W4M][GC-MS] CAMERA R Package - Preprocessing - Returns annotation results (isotope peaks, adducts and fragments)" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html Wrapper skript for automatic annotation of isotope peaks, adducts and fragments for a (grouped) xcmsSet xs. The function returns an xsAnnotate object. BEWARE: this tool don't come with its script. You will need to install the dedicated package_camara_w4m_script too" --category="Metabolomics"
--- a/tool_dependencies.xml	Mon Feb 22 17:09:43 2016 -0500
+++ b/tool_dependencies.xml	Sun Apr 10 08:14:59 2016 -0400
@@ -3,13 +3,10 @@
     <package name="R" version="3.1.2">
         <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="camera" version="1.22.0">
-        <repository changeset_revision="e7634e33ca20" name="package_r_camera_1_22_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="bioconductor-camera" version="1.22.0">
+        <repository changeset_revision="22cec61d66c2" name="package_bioconductor_camera_1_22_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="camera_w4m_script" version="2.2.1">
-        <repository changeset_revision="96606d74af08" name="package_camera_w4m_script_2_2_1" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="graphicsmagick" version="1.3.18">
-        <repository changeset_revision="9b0d84b880e4" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="graphicsmagick" version="1.3.20">
+        <repository changeset_revision="25002de17a97" name="package_graphicsmagick_1_3_20" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>