annotate pathview.r @ 3:f1691de443a7 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview commit a0d4b148fe03ed035ee3f746fb51ab67f4d08166"

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")

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)
  }
}