diff PSM2SAM.R @ 3:ce09f1a1bbad draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty

--- a/PSM2SAM.R	Thu Jan 14 18:13:18 2016 -0500
+++ b/PSM2SAM.R	Thu Jan 28 18:40:54 2016 -0500
@@ -32,18 +32,13 @@
 
 PSMtab2SAM <- function(
 	passedPSM_file = GalaxyInputFile(required=TRUE), 
-	exon_anno_file = GalaxyInputFile(),
-	proteinseq_file = GalaxyInputFile(),
-	procodingseq_file = GalaxyInputFile(),
-	header_file = GalaxyInputFile(),
+	exon_anno_file = GalaxyInputFile(required=TRUE),
+	proteinseq_file = GalaxyInputFile(required=TRUE),
+	procodingseq_file = GalaxyInputFile(required=TRUE),
+	header_file = GalaxyInputFile(required=TRUE),
 	XScolumn = GalaxyCharacterParam(required=TRUE), 
 	OutputFile = GalaxyOutput("proSAM","sam"))
 {
-    if (length(exon_anno_file) == 0) { exon_anno_file = paste(script_parent_dir, "tool-data/exon_anno.RData", sep="/") }
-    if (length(proteinseq_file) == 0) { proteinseq_file = paste(script_parent_dir, "tool-data/proseq.RData", sep="/") }
-    if (length(procodingseq_file) == 0) { procodingseq_file = paste(script_parent_dir, "tool-data/procodingseq.RData", sep="/") }
-    if (length(header_file) == 0) { header_file = paste(script_parent_dir, "tool-data/header_refseq_hg19.txt", sep="/") }
-
     if (!file.exists(header_file)) { gstop("failed to read header file") }
     if (file.exists(OutputFile))
     {
@@ -55,7 +50,7 @@
                 file.remove(OutputFile)
             }, error=function(err)
             {
-                gstop("failed to read empty existing file")
+                gstop("failed to remove empty existing file")
             })
         }
     }