Mercurial > repos > mmonsoor > probmetab

changeset 4:52b222a626b0 draft default tip

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planemo upload commit 00684d80f032fee5bd1cb86e05a477fcdcb1c3fc
author lecorguille
date Fri, 07 Apr 2017 09:11:22 -0400
parents abcfa1648b66
children
files lib.r
diffstat 1 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- 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)