# HG changeset patch
# User tomnl
# Date 1560870857 14400
# Node ID 68c405751ef64cb19f1bf250f4b54c59f9ca5e64
# Parent  b22aa0a9fc256f6eff45c87f78311cc0e8c088b1
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 14eafbdb65f491713d1314d77c454defd137c392

diff -r b22aa0a9fc25 -r 68c405751ef6 combineAnnotations.R
--- a/combineAnnotations.R	Tue Jun 18 10:08:40 2019 -0400
+++ b/combineAnnotations.R	Tue Jun 18 11:14:17 2019 -0400
@@ -47,32 +47,6 @@
 
 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
 
-if (!is.null(opt$eic)){
-
-  if (is.null(xset)){
-    xset <- xa@xcmsSet
-  }
-  # previous check should have matched filelists together
-  xset@filepaths <- unname(pa@fileList)
-
-  convert2Raw <- function(x, xset){
-    sid <- unique(x$sample)
-    # for each file get list of peaks
-    x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
-    x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])]
-    x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])]
-    return(x)
-
-  }
-
-  xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
-
-  # Saves the EICS into the previously created database
-  px <- msPurity::purityX(xset, saveEIC = TRUE,
-                          cores=1, sqlitePth=db_pth,
-                          rtrawColumns = TRUE)
-
-}
 
 closeAllConnections()
 
diff -r b22aa0a9fc25 -r 68c405751ef6 combineAnnotations.xml
--- a/combineAnnotations.xml	Tue Jun 18 10:08:40 2019 -0400
+++ b/combineAnnotations.xml	Tue Jun 18 11:14:17 2019 -0400
@@ -26,9 +26,7 @@
             #if $create_new_database:
               --create_new_database
             #end if
-            #if $eic
-                --eic
-            #end if
+
 
     ]]></command>
     <inputs>
@@ -48,10 +46,6 @@
                help="A copy will be made of the input SQLite spectral matching database and the results will be added to this copy.
                      When False, the input SQLite database will be updated the results. Use False
                      if you want to reduce storage space being used."/>
-       <param name="eic" type="boolean" label="Include EIC data?"
-               help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
-                     the database. Note, this will take considerable time for large datasets and
-                     the resulting SQLite database can be large"/>
     </inputs>
     <outputs>
         <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
diff -r b22aa0a9fc25 -r 68c405751ef6 createDatabase.R
--- a/createDatabase.R	Tue Jun 18 10:08:40 2019 -0400
+++ b/createDatabase.R	Tue Jun 18 11:14:17 2019 -0400
@@ -156,10 +156,10 @@
   }
 
   xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
-
+  closeAllConnections()
   # Saves the EICS into the previously created database
   px <- msPurity::purityX(xset, saveEIC = TRUE,
-                           cores=1, sqlitePth=db_pth,
+                           cores=1, sqlitePth=dbPth,
                            rtrawColumns = TRUE)
 
 }