From 06b079deef2cc4491297f7e8e2d942c611596797 Mon Sep 17 00:00:00 2001
From: gabrielctn <gabrielcretin@gmail.com>
Date: Sun, 8 Apr 2018 18:16:18 +0200
Subject: [PATCH] Added getInfos(mzfiles) function to complete output results

---
 galaxy/ipo/lib.r | 47 ++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 44 insertions(+), 3 deletions(-)

diff --git a/galaxy/ipo/lib.r b/galaxy/ipo/lib.r
index 42c499a..5986fa4 100644
--- a/galaxy/ipo/lib.r
+++ b/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)
 }