Mercurial > repos > proteore > proteore_clusterprofiler
changeset 31:b62fd03a3822 draft
planemo upload commit b636a89be85c5695c234abcf4960a731549ddd57-dirty
| author | proteore |
|---|---|
| date | Fri, 21 Dec 2018 03:55:25 -0500 |
| parents | eb12bb18b5dd |
| children | f2c0a2b44841 |
| files | GO-enrich.R cluster_profiler.xml |
| diffstat | 2 files changed, 14 insertions(+), 14 deletions(-) [+] |
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--- a/GO-enrich.R Tue Dec 18 03:21:33 2018 -0500 +++ b/GO-enrich.R Fri Dec 21 03:55:25 2018 -0500 @@ -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
--- a/cluster_profiler.xml Tue Dec 18 03:21:33 2018 -0500 +++ b/cluster_profiler.xml Fri Dec 21 03:55:25 2018 -0500 @@ -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> @@ -204,16 +204,15 @@ <element name="cluster_profiler_EGO_CC.csv" file="cluster_profiler_EGO_CC.csv" ftype="csv"/> <element name="cluster_profiler_EGO_BP.csv" file="cluster_profiler_EGO_BP.csv" ftype="csv"/> <element name="cluster_profiler_EGO_MF.csv" file="cluster_profiler_EGO_MF.csv" ftype="csv"/> - </output_collection> <output_collection name="graph_output"> - <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png" diff="size"/> - <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png" diff="size"/> - <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png" diff="size"/> - <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png" diff="size"/> - <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png" diff="size"/> - <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png" diff="size"/> - <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png" diff="size"/> + <element name="GGO_CC_bar-plot" file="GGO_CC_bar-plot" ftype="png"/> + <element name="GGO_BP_bar-plot" file="GGO_BP_bar-plot" ftype="png"/> + <element name="GGO_MF_bar-plot" file="GGO_MF_bar-plot" ftype="png"/> + <element name="EGO_CC_bar-plot" file="EGO_CC_bar-plot" ftype="png"/> + <element name="EGO_BP_bar-plot" file="EGO_BP_bar-plot" ftype="png"/> + <element name="EGO_CC_dot-plot" file="EGO_CC_dot-plot" ftype="png"/> + <element name="EGO_BP_dot-plot" file="EGO_BP_dot-plot" ftype="png"/> </output_collection> </test> </tests> @@ -231,7 +230,7 @@ ----- -**Input ** +**Input** Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) or by copy/pasting your IDs (separated by a space).