diff customProDB.R @ 9:328a1e3b5261 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty

--- a/customProDB.R	Mon May 09 12:55:26 2016 -0400
+++ b/customProDB.R	Wed Jun 08 14:04:54 2016 -0400
@@ -23,7 +23,12 @@
 option_list$proteinseq <- make_option('--proteinseq', type='character')
 option_list$procodingseq <- make_option('--procodingseq', type='character')
 option_list$ids <- make_option('--ids', type='character')
+option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character')
+option_list$cosmic <- make_option('--cosmic', type='character')
+option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE)
 option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
+#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE)
+#option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE)
 option_list$outputFile <- make_option('--outputFile', type='character')
 
 
@@ -37,14 +42,39 @@
 	exon_anno_file = GalaxyInputFile(required=TRUE),
 	proteinseq_file = GalaxyInputFile(required=TRUE),
 	procodingseq_file = GalaxyInputFile(required=TRUE),
+	ids_file = GalaxyInputFile(required=TRUE),
+	dbsnpinCoding_file = GalaxyInputFile(required=FALSE),
+	cosmic_file = GalaxyInputFile(required=FALSE),
+	annotationFromHistory = GalaxyLogicalParam(required=FALSE),
 	rpkmCutoff = GalaxyNumericParam(required=TRUE),
-	ids_file = GalaxyInputFile(required=TRUE),
+	#outputIndels = GalaxyLogicalParam(required=FALSE),
+	#outputNovelJunctions = GalaxyLogicalParam(required=FALSE),
 	outputFile = GalaxyOutput("FASTA","fasta"))
 {
-    file.symlink(exon_anno_file, "exon_anno.RData")
-    file.symlink(proteinseq_file, "proseq.RData")
-    file.symlink(procodingseq_file, "procodingseq.RData")
-    file.symlink(ids_file, "ids.RData")
+    file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/"))
+    file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/"))
+    file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/"))
+    file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/"))
+
+    if (length(dbsnpinCoding_file) > 0)
+    {
+        file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))
+        labelrsid = T
+    }
+    else
+    {
+        labelrsid = F
+    }
+
+    if (length(cosmic_file) > 0)
+    {
+        file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))
+        cosmic = T
+    }
+    else
+    {
+        cosmic = F
+    }
 
     bamLink = "input.bam"
     file.symlink(bam_file, bamLink)
@@ -52,9 +82,9 @@
 
     suppressPackageStartupMessages(library(customProDB))
 
-    easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file),
+    easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),
             rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
-            nov_junction=F, INDEL=T, lablersid=F, COSMIC=F)
+            nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic)
 }