Mercurial > repos > galaxyp > custom_pro_db_annotation_data_manager

annotate data_manager/customProDB_annotation.R @ 3:af0a098e15bd 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/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Wed, 27 Jan 2016 16:46:54 -0500
parents 20a1b026b798
children b42974daa659
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
1 #!/usr/bin/env Rscript
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
2
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
3 initial.options <- commandArgs(trailingOnly = FALSE)
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
5
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
6 ## begin warning handler
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
7 withCallingHandlers({
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
8
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
9 library(methods) # Because Rscript does not always do this
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
10
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
11 options('useFancyQuotes' = FALSE)
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
12
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
13 suppressPackageStartupMessages(library("optparse"))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
14 suppressPackageStartupMessages(library("RGalaxy"))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
15
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
16
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
17 option_list <- list()
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
18 option_list$dbkey <- make_option('--dbkey', type='character')
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
19 option_list$outputFile <- make_option('--outputFile', type='character')
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
20 option_list$dbkey_description <- make_option('--dbkey_description', type='character')
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
21
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
22 opt <- parse_args(OptionParser(option_list=option_list))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
23
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
24
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
25 customProDB_annotation <- function(
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
26 dbkey = GalaxyCharacterParam(required=TRUE),
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
27 dbkey_description = GalaxyCharacterParam(required=FALSE),
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
28 outputFile = GalaxyOutput("output","json"))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
29 {
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
30 if (!file.exists(outputFile))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
31 {
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
32 gstop("json params file does not exist")
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
33 }
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
34
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
35 if (length(dbkey_description) < 1)
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
36 {
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
37 dbkey_description = dbkey
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
38 }
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
39
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
40 suppressPackageStartupMessages(library(rjson))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
41 params = fromJSON(file=outputFile)
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
42 target_directory = params$output_data[[1]]$extra_files_path
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
43 dir.create(target_directory)
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
44
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
45 tryCatch(
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
46 {
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
47 file.remove(outputFile)
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
48 }, error=function(err)
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
49 {
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
50 gstop("failed to remove json params file after reading")
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
51 })
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
52
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
53 ucscTableCodingFastaURL = paste("http://genome.ucsc.edu/cgi-bin/hgTables?db=", dbkey, "&hgSeq.cdsExon=on&hgSeq.granularity=gene&hgSeq.casing=exon&hgSeq.repMasking=lower&hgta_doGenomicDna=get+sequence&hgta_group=genes&hgta_track=refGene&hgta_table=refGene&hgta_regionType=genome", sep="")
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
54 ucscTableProteinFastaURL = paste("http://genome.ucsc.edu/cgi-bin/hgTables?db=", dbkey, "&hgta_geneSeqType=protein&hgta_doGenePredSequence=submit&hgta_track=refGene&hgta_table=refGene", sep="")
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
55 codingFastaFilepath = paste(target_directory, "/", dbkey, ".cds.fa", sep="")
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
56 proteinFastaFilepath = paste(target_directory, "/", dbkey, ".protein.fa", sep="")
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
57
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
58 suppressPackageStartupMessages(library(customProDB))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
59 options(timeout=3600)
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
60
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
61 cat(paste("Downloading coding FASTA from:", ucscTableCodingFastaURL, "\n"))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
62 download.file(ucscTableCodingFastaURL, codingFastaFilepath, quiet=T, mode='wb')
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
63
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
64 cat(paste("Downloading protein FASTA from:", ucscTableProteinFastaURL, "\n"))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
65 download.file(ucscTableProteinFastaURL, proteinFastaFilepath, quiet=T, mode='wb')
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
66
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
67 cat(paste("Preparing Refseq annotation files\n"))
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
68 customProDB::PrepareAnnotationRefseq(genome=dbkey, CDSfasta=codingFastaFilepath, pepfasta=proteinFastaFilepath, annotation_path=target_directory)
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
69
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
70 outputPath = paste(dbkey, "/customProDB", sep="")
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
71 output = list(data_tables = list())
3
af0a098e15bd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents: 2
diff changeset
72 output[["data_tables"]][["customProDB"]]=c(path=outputPath, name=dbkey_description, dbkey=dbkey)
0
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
73 write(toJSON(output), file=outputFile)
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
74 }
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
75
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
76
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
77 params <- list()
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
78 for(param in names(opt))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
79 {
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
80 if (!param == "help")
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
81 params[param] <- opt[param]
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
82 }
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
83
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
84 setClass("GalaxyRemoteError", contains="character")
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
85 wrappedFunction <- function(f)
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
86 {
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
87 tryCatch(do.call(f, params),
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
88 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
89 }
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
90
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
91
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
92 suppressPackageStartupMessages(library(RGalaxy))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
93 do.call(customProDB_annotation, params)
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
94
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
95 ## end warning handler
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
96 }, warning = function(w) {
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
97 cat(paste("Warning:", conditionMessage(w), "\n"))
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
98 invokeRestart("muffleWarning")
663ee21a8609 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
galaxyp
parents:
diff changeset
99 })