# HG changeset patch
# User galaxyp
# Date 1462564567 14400
# Node ID b83a4002aab12d0cf4d8215953c1361401569ed9
# Parent  61e45c111ef754ce5f35948a497bdb44a204174e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty

diff -r 61e45c111ef7 -r b83a4002aab1 customProDB.R
--- 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)
 }
 
diff -r 61e45c111ef7 -r b83a4002aab1 customProDB.xml
--- a/customProDB.xml	Wed Feb 03 12:37:47 2016 -0500
+++ b/customProDB.xml	Fri May 06 15:56:07 2016 -0400
@@ -8,6 +8,7 @@
        --bam="$genome_annotation.bamInput"
        --bai="${genome_annotation.bamInput.metadata.bam_index}"
        --vcf="$genome_annotation.vcfInput"
+       --rpkmCutoff=$rpkmCutoff
        --outputFile="${output_rpkm}"
 
        #if str($genome_annotation.source) == "history":
@@ -64,6 +65,7 @@
         <param name="vcfInput" type="data" format="vcf" label="VCF file" />
       </when>
     </conditional>
+    <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." />
   </inputs>
   <outputs>
     <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>