diff customProDB.R @ 7:b83a4002aab1 draft

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

--- a/customProDB.R	Wed Feb 03 12:37:47 2016 -0500
+++ b/customProDB.R	Fri May 06 15:56:07 2016 -0400
@@ -23,6 +23,7 @@
 option_list$proteinseq <- make_option('--proteinseq', type='character')
 option_list$procodingseq <- make_option('--procodingseq', type='character')
 option_list$ids <- make_option('--ids', type='character')
+option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character')
 option_list$outputFile <- make_option('--outputFile', type='character')
 
 
@@ -36,6 +37,7 @@
 	exon_anno_file = GalaxyInputFile(required=TRUE),
 	proteinseq_file = GalaxyInputFile(required=TRUE),
 	procodingseq_file = GalaxyInputFile(required=TRUE),
+	rpkmCutoff = GalaxyNumericParam(required=TRUE),
 	ids_file = GalaxyInputFile(required=TRUE),
 	outputFile = GalaxyOutput("FASTA","fasta"))
 {
@@ -51,7 +53,7 @@
     suppressPackageStartupMessages(library(customProDB))
 
     easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file),
-            outfile_path=".", outfile_name="output",
+            rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",
             nov_junction=F, INDEL=T, lablersid=F, COSMIC=F)
 }