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comparison dexseq.R @ 5:278b189248cd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
author iuc
date Mon, 14 Jan 2019 05:02:19 -0500
parents 6e8b61c54ff3
children 62adf13b86ea
comparison
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4:251393b72616 5:278b189248cd
19 'verbose', 'v', 2, "integer", 19 'verbose', 'v', 2, "integer",
20 'help', 'h', 0, "logical", 20 'help', 'h', 0, "logical",
21 'gtf', 'a', 1, "character", 21 'gtf', 'a', 1, "character",
22 'outfile', 'o', 1, "character", 22 'outfile', 'o', 1, "character",
23 'reportdir', 'r', 1, "character", 23 'reportdir', 'r', 1, "character",
24 'rds', 'd', 1, "character",
24 'factors', 'f', 1, "character", 25 'factors', 'f', 1, "character",
25 'threads', 'p', 1, "integer", 26 'threads', 'p', 1, "integer",
26 'fdr', 'c', 1, "double" 27 'fdr', 'c', 1, "double"
27 ), byrow=TRUE, ncol=4); 28 ), byrow=TRUE, ncol=4);
28 opt = getopt(spec); 29 opt = getopt(spec);
108 export_table[i,last_column] <- paste(export_table[i,last_column][[1]],collapse=", ") 109 export_table[i,last_column] <- paste(export_table[i,last_column][[1]],collapse=", ")
109 } 110 }
110 write.table(export_table, file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE) 111 write.table(export_table, file = opt$outfile, sep="\t", quote = FALSE, col.names = FALSE)
111 print("Written Results") 112 print("Written Results")
112 113
114 if ( !is.null(opt$rds) ) {
115 saveRDS(res, file="DEXSeqResults.rds")
116 }
117
113 if ( !is.null(opt$reportdir) ) { 118 if ( !is.null(opt$reportdir) ) {
114 save(dxd, resSorted, file = file.path(opt$reportdir,"DEXSeq_analysis.RData"))
115 save.image()
116 DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA")) 119 DEXSeqHTML(res, fitExpToVar=primaryFactor, path=opt$reportdir, FDR=opt$fdr, color=c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7","#CEAEFF", "#EDC3C5", "#AAA8AA"))
117 unlink(file.path(opt$reportdir,"DEXSeq_analysis.RData"))
118 } 120 }
119 sessionInfo() 121 sessionInfo()