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Commit message:
planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty |
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modified:
GO-enrich.R cluster_profiler.xml |
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| diff -r 4609346d8108 -r b29255864039 GO-enrich.R --- a/GO-enrich.R Tue Dec 18 09:21:32 2018 -0500 +++ b/GO-enrich.R Fri Dec 21 04:12:32 2018 -0500 |
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| @@ -152,13 +152,14 @@ argsDF <- as.data.frame(do.call("rbind", parseArgs(args))) args <- as.list(as.character(argsDF$V2)) names(args) <- argsDF$V1 + + #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda") + #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda") + plot = unlist(strsplit(args$plot,",")) go_represent=str2bool(args$go_represent) go_enrich=str2bool(args$go_enrich) - #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda") - #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda") - suppressMessages(library(args$species, character.only = TRUE, quietly = TRUE)) # Extract OrgDb @@ -232,7 +233,7 @@ # Get file content universe_file = read_file(universe_filename, universe_header) # Extract Protein IDs list - universe <- sapply(universe_file[,universe_ncol], function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE) + universe <- unlist(sapply(universe_file[,universe_ncol], function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE)) } universe_id_type = args$universe_id_type ##to initialize |
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| diff -r 4609346d8108 -r b29255864039 cluster_profiler.xml --- a/cluster_profiler.xml Tue Dec 18 09:21:32 2018 -0500 +++ b/cluster_profiler.xml Fri Dec 21 04:12:32 2018 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.18"> +<tool id="cluter_profiler" name="GO terms classification and enrichment analysis" version="2018.12.21"> <description>(Human, Mouse, Rat)[clusterProfiler]</description> <requirements> <requirement type="package" version="3.4.1">R</requirement> |