# HG changeset patch
# User tomnl
# Date 1531908392 14400
# Node ID 78885fff83a3f6483ceda5482b9d86d0e9c000b6
# Parent  49e0630706475814c88981f91045d718804f1fb0
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875

diff -r 49e063070647 -r 78885fff83a3 create_msp.R
--- a/create_msp.R	Tue Jul 17 12:30:24 2018 -0400
+++ b/create_msp.R	Wed Jul 18 06:06:32 2018 -0400
@@ -21,11 +21,11 @@
 
 
 
+#grped_df$fileid <- sapply(grped_df$filename, function(x) which(basename(pa@fileList)==x))
+#puritydf$fileid <- sapply(puritydf$filename, function(x) which(basename(pa@fileList)==x))
 
 
-grped_df$fileid <- sapply(grped_df$filename, function(x) which(basename(pa@fileList)==x))
 
-puritydf$fileid <- sapply(puritydf$filename, function(x) which(basename(pa@fileList)==x))
 
 selfrag <- as.numeric(unique(grped_df$grpid)) 
 
@@ -66,9 +66,15 @@
 
                 specj <- spec[[jj]]
 
-                grpdj <- grpd[jj,]
+
 
-                name = paste(i, grpdj$sample, grpdj$pid, sep='-')
+                grpdj <- grpd[jj,]
+                if ('sample' %in% colnames(grpd)){
+                    fileid = grpdj$sample
+                }else{
+                    fileid = grpdj$fileid
+                }
+                name = paste(i, fileid, grpdj$pid, sep='-')
 
                 write.msp(name,grpdj$precurMtchMZ,"",specj,of)
             }
@@ -82,7 +88,13 @@
                 idx <- which(prec_int==max(prec_int))
 
                 grpd <- grpd[idx,]
-                name = paste(i, grpd$sample, grpd$pid, sep='-')
+                if ('sample' %in% colnames(grpd)){
+                    fileid = grpd$sample
+                }else{
+                    fileid = grpd$fileid
+                }
+
+                name = paste(i, fileid, grpd$pid, sep='-')
                 write.msp(name,grpd$precurMtchMZ,"",specj[[idx]], of)
             }
 
@@ -175,7 +187,12 @@
         spec <- spec[[1]]
 
         grpd <- grped_df[j,]
-        name = paste(i, grpd$sample, grpd$pid, sep='-')
+        if ('sample' %in% colnames(grpd)){
+            fileid = grpd$sample
+        }else{
+            fileid = grpd$fileid
+        }
+        name = paste(i, fileid, grpd$pid, sep='-')
         write.msp(name,grpd$precurMtchMZ,"",spec,of)
     }
 }
diff -r 49e063070647 -r 78885fff83a3 create_msp.xml
--- a/create_msp.xml	Tue Jul 17 12:30:24 2018 -0400
+++ b/create_msp.xml	Wed Jul 18 06:06:32 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="create_msp" name="Create MSP Files from msPurity" version="0.1.2">
+<tool id="create_msp" name="Create MSP Files from msPurity" version="0.1.3">
     <description> </description>
      <macros>
         <import>macros.xml</import>