Mercurial > repos > galaxyp > custom_pro_db

annotate customProDB.R @ 3:7e078d4e40f8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Fri, 29 Jan 2016 14:26:25 -0500
parents
children 61e45c111ef7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
1 #!/usr/bin/env Rscript
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
2
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
3 initial.options <- commandArgs(trailingOnly = FALSE)
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
5
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
6 ## begin warning handler
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
7 withCallingHandlers({
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
8
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
9 library(methods) # Because Rscript does not always do this
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
10
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
11 options('useFancyQuotes' = FALSE)
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
12
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
13 suppressPackageStartupMessages(library("optparse"))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
14 suppressPackageStartupMessages(library("RGalaxy"))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
15
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
16
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
17 option_list <- list()
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
18
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
19 option_list$bam <- make_option('--bam', type='character')
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
20 option_list$vcf <- make_option('--vcf', type='character')
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
21 option_list$exon_anno <- make_option('--exon_anno', type='character')
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
22 option_list$proteinseq <- make_option('--proteinseq', type='character')
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
23 option_list$procodingseq <- make_option('--procodingseq', type='character')
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
24 option_list$outputFile <- make_option('--outputFile', type='character')
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
25
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
26
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
27 opt <- parse_args(OptionParser(option_list=option_list))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
28
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
29
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
30 customProDB <- function(
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
31 bam_file = GalaxyInputFile(required=TRUE),
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
32 vcf_file = GalaxyInputFile(required=TRUE),
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
33 exon_anno_file = GalaxyInputFile(required=TRUE),
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
34 proteinseq_file = GalaxyInputFile(required=TRUE),
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
35 procodingseq_file = GalaxyInputFile(required=TRUE),
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
36 outputFile = GalaxyOutput("FASTA","fasta"))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
37 {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
38 if (dirname(exon_anno_file) != dirname(proteinseq_file) ||
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
39 dirname(exon_anno_file) != dirname(procodingseq_file))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
40 {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
41 gstop("parent directory of annotation files must all be the same")
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
42 }
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
43
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
44 if (file.exists(outputFile))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
45 {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
46 if (file.info(outputFile)$size > 0) { gstop("output file already exists") }
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
47 else
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
48 {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
49 tryCatch(
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
50 {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
51 file.remove(outputFile)
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
52 }, error=function(err)
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
53 {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
54 gstop("failed to remove empty existing file")
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
55 })
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
56 }
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
57 }
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
58
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
59 suppressPackageStartupMessages(library(customProDB))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
60
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
61 easyRun(bamFile=bamFile, vcfFile=vcfFile, annotation_path=dirname(exon_anno_file), outfile_path=dirname(outputFile), outfile_name=basename(outputFile))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
62 }
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
63
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
64
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
65 params <- list()
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
66 for(param in names(opt))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
67 {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
68 if (!param == "help")
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
69 params[param] <- opt[param]
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
70 }
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
71
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
72 setClass("GalaxyRemoteError", contains="character")
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
73 wrappedFunction <- function(f)
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
74 {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
75 tryCatch(do.call(f, params),
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
76 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
77 }
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
78
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
79
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
80 suppressPackageStartupMessages(library(RGalaxy))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
81 do.call(customProDB, params)
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
82
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
83 ## end warning handler
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
84 }, warning = function(w) {
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
85 cat(paste("Warning:", conditionMessage(w), "\n"))
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
86 invokeRestart("muffleWarning")
7e078d4e40f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
87 })