# HG changeset patch
# User lecorguille
# Date 1491570682 14400
# Node ID 52b222a626b0c5951797192970e4a9c231ebde13
# Parent  abcfa1648b6612adb56947fd301613b94606eff5
planemo upload commit 00684d80f032fee5bd1cb86e05a477fcdcb1c3fc

diff -r abcfa1648b66 -r 52b222a626b0 lib.r
--- a/lib.r	Fri Apr 07 07:14:12 2017 -0400
+++ b/lib.r	Fri Apr 07 09:11:22 2017 -0400
@@ -122,7 +122,7 @@
     ansConn = export.class.table(conn, reactionM, ionAnnot, DB=DB,html=listArguments[["html"]],filename="AnalysisExample",prob=listArguments[["prob"]])
     if(listArguments[["html"]]){
         #Zip the EICS plot
-        system(paste('zip -r "Analysis_Report.zip" "AnalysisExample_fig"'))
+        system(paste('zip -rq "Analysis_Report.zip" "AnalysisExample_fig"'))
     }
 
     # calculate the correlations and partial correlations and cross reference then with reactions
@@ -148,10 +148,10 @@
         write.table(variableM, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata.tsv")
     } else if (listArguments[["mode_acquisition"]]=="two") {
         #Retrocompatibility with previous annotateDiffreport variableMetadata dataframe (must replace mzmed column by mz, and rtmed by rt)
-        names(variableMetadataP)[names(variableMetadata)=="mzmed"] <- "mz"
-        names(variableMetadataP)[names(variableMetadata)=="rtmed"] <- "rt"
-        names(variableMetadataN)[names(variableMetadata)=="mzmed"] <- "mz"
-        names(variableMetadataN)[names(variableMetadata)=="rtmed"] <- "rt"
+        names(variableMetadataP)[names(variableMetadataP)=="mzmed"] <- "mz"
+        names(variableMetadataP)[names(variableMetadataP)=="rtmed"] <- "rt"
+        names(variableMetadataN)[names(variableMetadataN)=="mzmed"] <- "mz"
+        names(variableMetadataN)[names(variableMetadataN)=="rtmed"] <- "rt"
         variableMP=merge_probmetab(variableMetadataP, ansConn)
         write.table(variableMP, sep="\t", quote=FALSE, row.names=FALSE, file="variableMetadata_Positive.tsv")
         variableMN=merge_probmetab(variableMetadataN, ansConn)