# HG changeset patch # User iuc # Date 1566844972 14400 # Node ID bd99e8fbde97c08eb9325285d97ac48a769985c7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit 438c20a62c01fa4adea6fbb4cb40ae05b4166043" diff -r 000000000000 -r bd99e8fbde97 pathview.r --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pathview.r Mon Aug 26 14:42:52 2019 -0400 @@ -0,0 +1,89 @@ +options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) + +# we need that to not crash galaxy with an UTF8 error on German LC settings. +loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") + +suppressPackageStartupMessages({ + library("pathview") + library("optparse") +}) + +sessionInfo() + +option_list <- list( + make_option(c("--pathway_id"), type="character", default=NULL, help="Path to tabular file with gene data"), + make_option(c("--pathway_id_fp"), type="character", default=NULL, help="Path to tabular file with pathway ids"), + make_option(c("--pathway_id_header"), type="logical", default=FALSE, help="Header for tabular file with pathway ids"), + make_option(c("--species"), type="character", default="hsa", help="KEGG code, scientific name or the common name of the species"), + make_option(c("--gene_data"), type="character", default=NULL, help="Path to tabular file with gene data"), + make_option(c("--gd_header"), type="logical", default=FALSE, help="Header for the gene data file"), + make_option(c("--gene_idtype"), type="character", default="entrez", help="ID type used for the gene data"), + make_option(c("--cpd_data"), type="character", default=NULL, help="Path to tabular file with compound data"), + make_option(c("--cpd_header"), type="logical", default=FALSE, help="Header for the compound data file"), + make_option(c("--cpd_idtype"), type="character", default="kegg", help="ID type used for the compound data"), + make_option(c("--multi_state"), type="logical", default=TRUE, help="Are the gene and compound data paired?"), + make_option(c("--match_data"), type="logical", default=TRUE, help="Are the gene and compound data paired?"), + make_option(c("--kegg_native"), type="logical", default=TRUE, help="Render pathway graph as native KEGG grap? Alternative is the Graphviz layout"), + make_option(c("--same_layer"), type="logical", default=TRUE, help="Plot on same layer?"), + make_option(c("--map_null"), type="logical", default=TRUE, help="Map the NULL gene or compound data to pathway?"), + make_option(c("--split_group"), type="logical", default=FALSE, help="Split node groups into individual nodes?"), + make_option(c("--expand_node"), type="logical", default=FALSE, help="Expand multiple-gene nodes into single-gene nodes?"), + make_option(c("--sign_pos"), type="character", default="bottomright", help="Position of pathview signature") +) + +parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) +args = parse_args(parser) +print(args) + +read_table = function(fp, header, rownames=1, colclasses=NA){ + table = read.table(fp, header=header, sep="\t", row.names=rownames, colClasses=colclasses) + # transform to vector if only one column + if(dim(table)[2] == 1){ + names = rownames(table) + table = table[,1] + names(table) = names + } + return(table) +} + +get_table = function(fp, header){ + table = NULL + if(!is.null(fp)){ + table = read_table(fp, header, rownames=1) + } + return(table) +} + +# load gene_data file +gene_data = get_table(args$gene_data, args$gd_header) + +# load compound data file +cpd_data = get_table(args$cpd_data, args$cpd_header) + +run_pathview = function(pathway_id){ + pathview( + pathway.id=pathway_id, + gene.data=gene_data, + gene.idtype=args$gene_idtype, + cpd.data=cpd_data, + cpd.idtype=args$cpd_idtype, + species=args$species, + multi.state=args$multi_state, + match.data=args$match_data, + kegg.native=args$kegg_native, + same.layer=args$same_layer, + split.group=args$split_group, + expand.node=args$expand_node, + sign.pos=args$sign_pos, + map.null=args$map_null) +} + +# get pathway ids +if(!is.null(args$pathway_id)){ + run_pathview(args$pathway_id) +} else { + pthws = read_table(args$pathway_id_fp, args$pathway_id_header, rownames=NULL, colclasses="character") + for(p in pthws){ + run_pathview(p) + } +} diff -r 000000000000 -r bd99e8fbde97 pathview.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pathview.xml Mon Aug 26 14:42:52 2019 -0400 @@ -0,0 +1,405 @@ + + for pathway based data integration and visualization + + 1.24.0 + galaxy0 + + + bioconductor-pathview + bioconductor-org.ag.eg.db + bioconductor-org.at.tair.db + bioconductor-org.bt.eg.db + bioconductor-org.ce.eg.db + bioconductor-org.cf.eg.db + bioconductor-org.dm.eg.db + bioconductor-org.dr.eg.db + bioconductor-org.eck12.eg.db + bioconductor-org.ecsakai.eg.db + bioconductor-org.gg.eg.db + bioconductor-org.hs.eg.db + bioconductor-org.mm.eg.db + bioconductor-org.mmu.eg.db + bioconductor-org.pf.plasmo.db + bioconductor-org.pt.eg.db + bioconductor-org.rn.eg.db + bioconductor-org.sc.sgd.db + bioconductor-org.ss.eg.db + bioconductor-org.xl.eg.db + r-optparse + + /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]> + + + + + + + + + + ^(?:\d\d\d\d\d)?$ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + + + +
+
+ + + pathway['nb'] == 'one' + out['kegg_native']['out'] == 'TRUE' + + + pathway['nb'] == 'one' + out['kegg_native']['out'] == 'FALSE' + + + pathway['nb'] == 'multiple' + out['kegg_native']['out'] == 'TRUE' + + + + pathway['nb'] == 'multiple' + out['kegg_native']['out'] == 'FALSE' + + + + + + + + + + + + + + + + + + + + + +
+ + + + + +
+ +
+ + + + + + + + + + + + + + + + + +
+ + + + + + + +
+ +
+ + + + + + + + + + + + + + + + + + +
+ + + + + +
+ + + + +
+ + + + + + + + + + + + + + + + + + + + + +
+ + + + + + + +
+ + + + +
+
+ + + 10.1093/bioinformatics/btt285 + +
\ No newline at end of file diff -r 000000000000 -r bd99e8fbde97 static/images/dme00010_graphviz.png Binary file static/images/dme00010_graphviz.png has changed diff -r 000000000000 -r bd99e8fbde97 static/images/dme00010_native.png Binary file static/images/dme00010_native.png has changed diff -r 000000000000 -r bd99e8fbde97 test-data/cpd_data.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cpd_data.tabular Mon Aug 26 14:42:52 2019 -0400 @@ -0,0 +1,3000 @@ +C00232 -1.09759771890052 +C01881 0.128915365792426 +C02424 2.0785102666558 +C07418 0.932992454258254 +C13756 -0.00786047983581522 +C07378 -0.0902330032505592 +C06633 -1.00197436914991 +C00251 2.66218643563674 +C01059 -1.85078956265821 +C02226 -0.135552037249008 +C03037 -1.5832744194994 +C10017 0.951442661753311 +C05590 0.0389748404326761 +C04221 1.86546245325154 +C03725 0.677275239341894 +C08817 1.93743611595937 +C12058 -0.617105151942241 +C11718 -0.374217547892271 +C00665 0.57083478439713 +C06921 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