Mercurial > repos > iuc > pathview

changeset 2:fe154a7af404 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit f21f5effc122e992ed977bc42b27f9520f59a33b"
author iuc
date Fri, 08 Apr 2022 15:36:51 +0000
parents 03c13085aecc
children f1691de443a7
files pathview.r pathview.xml
diffstat 2 files changed, 63 insertions(+), 56 deletions(-) [+]
line wrap: on
line diff
--- a/pathview.r	Thu Jan 23 08:01:06 2020 -0500
+++ b/pathview.r	Fri Apr 08 15:36:51 2022 +0000
@@ -1,4 +1,8 @@
-options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+error_foo <- function() {
+  cat(geterrmessage(), file = stderr());
+  q("no", 1, F)
+}
+options(show.error.messages = F, error = error_foo)
 
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
@@ -11,79 +15,79 @@
 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")
+  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)
+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)
+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
+  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)
+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)
+gene_data <- get_table(args$gene_data, args$gd_header)
 
 # load compound data file
-cpd_data = get_table(args$cpd_data, args$cpd_header)
+cpd_data <- get_table(args$cpd_data, args$cpd_header)
 
-run_pathview = function(pathway_id){
+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$map_null)
+    pathway.id = pathway_id,
+    gene.data = gene_data,
+    gene.idtype = args$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$pathway_id)){
+if (!is.null(args$pathway_id)) {
   run_pathview(args$pathway_id)
 } else {
-  pthws = read_table(args$pathway_id_fp, args$pathway_id_header, rownames=NULL, colclasses="character")
-  for(p in pthws){
+  pthws <- read_table(args$pathway_id_fp, args$pathway_id_header, rownames = NULL, colclasses = "character")
+  for (p in pthws) {
     run_pathview(p)
   }
 }
--- a/pathview.xml	Thu Jan 23 08:01:06 2020 -0500
+++ b/pathview.xml	Fri Apr 08 15:36:51 2022 +0000
@@ -1,11 +1,14 @@
-<tool id="pathview" name="Pathview" version="@VERSION@+@GALAXY_VERSION@">
+<tool id="pathview" name="Pathview" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>for pathway based data integration and visualization</description>
+    <xrefs>
+        <xref type="bio.tools">pathview</xref>
+    </xrefs>
     <macros>
-        <token name="@VERSION@">1.24.0</token>
-        <token name="@GALAXY_VERSION@">galaxy0</token>
+        <token name="@TOOL_VERSION@">1.24.0</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <requirements>
-        <requirement type="package" version="@VERSION@">bioconductor-pathview</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-pathview</requirement>
         <requirement type="package" version="3.8.2">bioconductor-org.ag.eg.db</requirement>
         <requirement type="package" version="3.8.2">bioconductor-org.at.tair.db</requirement>
         <requirement type="package" version="3.8.2">bioconductor-org.bt.eg.db</requirement>
@@ -82,7 +85,7 @@
                 </param>
             </when>
             <when value="multiple">
-                <param name="tabular" type="data" format="tabular" optional="true" label="KEGG pathways" help="A table with one-column with KEGG pathways to plot"/>
+                <param name="tabular" type="data" format="txt,tabular" optional="true" label="KEGG pathways" help="A table with one-column with KEGG pathways to plot"/>
                 <param name="header" type="boolean" checked="true" label="Does the file have header (a first line with column names)?"/>
             </when>
         </conditional>