Dev - Fixes / Improvements / Changes

galaxy/ipo/ipo4retgroup.r

@@ -1,6 +1,8 @@
 #!/usr/bin/env Rscript
 #Authors Gildas Le Corguille and Yann Guitton
 
+# Setup R error handling to go to stderr for better error messages in Galaxy
+options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
 
 # ----- LOG FILE -----
 log_file=file("log.txt", open = "wt")
@@ -42,8 +44,6 @@ source_local("lib.r")
 
 cat("\n\n")
 
-#Import the different functions
-
 # ----- PROCESSING INFILE -----
 cat("\tARGUMENTS PROCESSING INFO\n")
 
@@ -68,8 +68,8 @@ if (!is.null(listArguments[["zipfile"]])){
 
 
 if (!is.null(listArguments[["singlefile_galaxyPath"]])){
-    singlefile_galaxyPath = unlist(strsplit(listArguments[["singlefile_galaxyPath"]],",")); listArguments[["singlefile_galaxyPath"]]=NULL
-    singlefile_sampleName = unlist(strsplit(listArguments[["singlefile_sampleName"]],",")); listArguments[["singlefile_sampleName"]]=NULL
+  singlefile_galaxyPath = listArguments[["singlefile_galaxyPath"]]; listArguments[["singlefile_galaxyPath"]]=NULL
+  singlefile_sampleName = listArguments[["singlefile_sampleName"]]; listArguments[["singlefile_sampleName"]]=NULL
 }
 
 # single file case

galaxy/ipo/ipo4retgroup.xml

@@ -21,6 +21,12 @@
         LANG=C Rscript $__tool_directory__/ipo4retgroup.r
 
         image '$image'
+
+        #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
+            singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
+        #else
+            zipfile '$input'
+        #end if
 
         parametersOutput '$parametersOutput'
 
@@ -41,19 +47,19 @@
 
         ## retcor methods
 
-        #if $retcor.methods.method == "obiwarp":
+        #if $retcor.methods.retcormethod == "obiwarp":
             retcorMethod obiwarp
-            profStep $methods.section_retcor_obiwarp_non_optimizable.profStep
+            profStep $retcor.methods.section_retcor_obiwarp_non_optimizable.profStep
 
-        #elif $retcor.methods.method == "peakgroups":
+        #elif $retcor.methods.retcormethod == "peakgroups":
             retcorMethod loess
             smooth $retcor.methods.section_retcor_peakgroups_non_optimizable.smooth
             extra $retcor.methods.section_retcor_peakgroups_non_optimizable.extra
             missing $retcor.methods.section_retcor_peakgroups_non_optimizable.missing
             span $retcor.methods.section_retcor_peakgroups_non_optimizable.span
             family $retcor.methods.section_retcor_peakgroups_non_optimizable.family
             plottype $retcor.methods.section_retcor_peakgroups_non_optimizable.plottype
-        #elif $retcor.methods.method == "none":
+        #elif $retcor.methods.retcormethod == "none":
             retcorMethod none
         #end if
 
@@ -63,6 +69,8 @@
     ]]></command>
 
     <inputs>
+
+        <param name="input" type="data" format="mzxml,mzml,mzdata,netcdf,no_unzip.zip,zip" label="File(s) from your history containing your chromatograms" help="Single file mode for the format: mzxml, mzml, mzdata and netcdf. Zip file mode for the format: no_unzip.zip, zip. See the help section below." />
 
         <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
 
@@ -104,8 +112,8 @@
 
         <section name="retcor" title="Retcor Options" expanded="True">
             <conditional name="methods">
-                <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
-                    <option value="obiwarp">obiwarp</option>
+                <param name="retcormethod" type="select" label="Method to use for retention time correction" help="[method] See the help section below" >
+                    <option value="obiwarp" selected="true">obiwarp</option>
                     <option value="peakgroups">peakgroups</option>
                 </param>
                 <when value="obiwarp">
@@ -179,7 +187,7 @@
             </section>
             <section name="retcor">
                 <conditional name="methods">
-                    <param name="method" value="peakgroups"/>
+                    <param name="retcormethod" value="peakgroups"/>
                     <section name="section_retcor_peakgroups_non_optimizable">
                         <param name="smooth" value="loess"/>
                         <param name="rextra" value="1"/>

galaxy/ipo/ipo4xcmsSet.r

@@ -1,6 +1,8 @@
 #!/usr/bin/env Rscript
 #Authors Gildas Le Corguille and Yann Guitton
 
+# Setup R error handling to go to stderr for better error messages in Galaxy
+options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
 
 # ----- LOG FILE -----
 log_file=file("log.txt", open = "wt")
@@ -18,7 +20,7 @@ for(pkg in pkgs) {
   cat(pkg,"\t",as.character(packageVersion(pkg)),"\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"); 
+cat("\n\n");
 
 
 
@@ -82,15 +84,15 @@ if(exists("singlefile_galaxyPath") && (singlefile_galaxyPath!="")) {
         error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
         print(error_message); stop(error_message)
     }
-    
+
     cwd=getwd()
     dir.create("raw")
     setwd("raw")
     file.symlink(singlefile_galaxyPath,singlefile_sampleName)
     setwd(cwd)
-    
+
     directory = "raw"
-    
+
 }
 
 # We unzip automatically the chromatograms from the zip files.
@@ -109,7 +111,7 @@ if(exists("zipfile") && (zipfile!="")) {
     setwd("ipoworkingdir")
 
     #unzip
-    suppressWarnings(unzip(zipfile, unzip="unzip"))
+    suppressWarnings(unzip(zipfile, unzip=getOption("unzip")))
 
     #get the directory name
     filesInZip=unzip(zipfile, list=T);
@@ -160,4 +162,3 @@ cat("\n\n")
 
 
 cat("\tDONE\n")
-

galaxy/ipo/lib.r

@@ -1,3 +1,22 @@
+getInfos = function(mzdatafiles){
+
+  # Get informations about instruments used and run
+  file.format = c("mzData", "mzdata")
+  if(tools::file_ext(mzdatafiles) %in% file.format){
+    ms = openMSfile(mzdatafiles, backend="Ramp")
+  } else {
+    ms = openMSfile(mzdatafiles)
+  }
+
+  runInfo = t(sapply(runInfo(ms), function(x) x[1], USE.NAMES=TRUE))
+  instrumentInfo = t(sapply(instrumentInfo(ms), function(x) x, USE.NAMES=TRUE))
+
+  infos = list("runinfo" = runInfo, "instrumentInfo" = instrumentInfo)
+  return (infos)
+}
+
+
+
 ##
 ## This function launch IPO functions to get the best parameters for xcmsSet
 ## A sample among the whole dataset is used to save time
@@ -32,13 +51,35 @@ ipo4xcmsSet = function(directory, parametersOutput, listArguments, samplebyclass
     # filter listArguments to only get releavant parameters and complete with those that are not declared
     peakpickingParametersUser = c(listArguments[names(listArguments) %in% names(peakpickingParameters)], peakpickingParameters[!(names(peakpickingParameters) %in% names(listArguments))])
     peakpickingParametersUser$verbose.columns = TRUE
+
+    # allow range for min and max peakwidth and ppm if given in arguments
+  if (!is.null(listArguments[["minPeakWidth"]])){
+    peakpickingParametersUser$min_peakwidth = as.vector(as.numeric(unlist(strsplit(listArguments[["minPeakWidth"]],split = ","))))
+    listArguments[["minPeakWidth"]] = NULL
+  }
+
+  if (!is.null(listArguments[["maxPeakWidth"]])){
+    peakpickingParametersUser$max_peakwidth = as.vector(as.numeric(unlist(strsplit(listArguments[["maxPeakWidth"]],split = ","))))
+    listArguments[["maxPeakWidth"]] = NULL 
+  }
+
+  if (!is.null(listArguments[["ppm"]])){
+    if(grepl(",", listArguments[["ppm"]]))
+      peakpickingParametersUser$ppm = as.vector(as.numeric(unlist(strsplit(listArguments[["ppm"]],split = ","))))
+    else
+      peakpickingParametersUser$ppm = listArguments[["ppm"]]
+    listArguments[["ppm"]] = NULL
+  }
 
     #peakpickingParametersUser$profparam <- list(step=0.005) #not yet used by IPO have to think of it for futur improvement
     resultPeakpicking = optimizeXcmsSet(mzmlfile, peakpickingParametersUser, nSlaves=peakpickingParametersUser$nSlaves, subdir="../IPO_results") #some images generated by IPO
 
-    # export
-    resultPeakpicking_best_settings_parameters = resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves","verbose.columns"))]
-    write.table(t(as.data.frame(resultPeakpicking_best_settings_parameters)), file=parametersOutput,  sep="\t", row.names=T, col.names=F, quote=F)  #can be read by user
+    # export results
+  resultPeakpicking_best_settings_parameters = resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves","verbose.columns"))]
+
+  infos = getInfos(mzmlfile)
+  # Write results in table with machine and run infos
+  write.table(cbind(mzmlfile, infos$instrumentInfo, infos$runInfo, t(as.matrix(resultPeakpicking_best_settings_parameters))), file=parametersOutput,  sep="\t", row.names=F, col.names=T, quote=F)
 
     return (resultPeakpicking$best_settings$xset)
 }