Mercurial > repos > proteore > proteore_maps_visualization
changeset 4:8e611bdc96ec draft
"planemo upload commit 6bef056b0e52bfa39dbe8591bfe67f8c95bf3ba2-dirty"
author | proteore |
---|---|
date | Wed, 15 Jan 2020 11:31:03 -0500 |
parents | dfceadc0b703 |
children | 4a3056be0774 |
files | kegg_maps_visualization.R kegg_maps_visualization.xml |
diffstat | 2 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/kegg_maps_visualization.R Fri Jun 28 05:16:30 2019 -0400 +++ b/kegg_maps_visualization.R Wed Jan 15 11:31:03 2020 -0500 @@ -85,8 +85,8 @@ get_ref_pathways <- function(species){ ##all available pathways for the species - pathways <-keggLink("pathway", species) - tot_path<-unique(pathways) + pathways <- keggLink("pathway", species) + tot_path <- unique(pathways) ##formating the dat into a list object ##key= pathway ID, value = genes of the pathway in the kegg format @@ -238,6 +238,7 @@ pathways_file = read_file(args$pathways_input,header2) ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) } + if (args$native_kegg) { ids <- ids[ids != "04215"] } pathways_list <- read_file(args$pathways_list,F) if (!is.null(args$id_list)) { id_list <- get_list_from_cp(args$id_list)
--- a/kegg_maps_visualization.xml Fri Jun 28 05:16:30 2019 -0400 +++ b/kegg_maps_visualization.xml Wed Jan 15 11:31:03 2020 -0500 @@ -1,8 +1,9 @@ -<tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.06.27.1"> +<tool id="kegg_maps_visualization" name="Pathways visualization" version="2020.01.08"> <description>of (differentially expressed) genes/proteins [KEGG]</description> <requirements> - <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> - <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> + <requirement type="package" version="3.6.2" >R</requirement> + <requirement type="package" version="1.26.0">bioconductor-pathview</requirement> + <requirement type="package" version="1.26.0">bioconductor-keggrest</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript $__tool_directory__/kegg_maps_visualization.R