## gencode_annotation
script <- "
species=$1
version=$2
wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_$species/release_$version/gencode.v$version.annotation.gtf.gz
gzip -d gencode.v$version.annotation.gtf.gz
"
gencode_annotation <- recipeMake(shscript = script,
paramID = c("species", "version"),
paramType = c("string", "string"),
outputID = "annotation",
outputGlob = "gencode.v*.annotation.gtf"
)
gencode_annotation <- addMeta(
cwl = gencode_annotation,
label = "gencode_annotation",
doc = "Download and unzip annotation files from gencode",
inputLabels = c("species", "version"),
inputDocs = c("'human' or 'mouse'",
paste0("Character string. Case sensitive. ",
"must match available versions for each species under source URL link. ",
"e.g., 'M31' (species='mouse'), '42' (species='human') ")),
outputLabels = c("annotation"),
outputDocs = c("the unzipped annotation file: `gencode.v$version.annotation.gtf`"),
extensions = list(
author = "rworkflow team",
url = "http://ftp.ebi.ac.uk/pub/databases/gencode/",
date = Sys.Date(),
example = paste(
"## Get data from evaluting recipe",
"gencode_annotation <- recipeLoad('gencode_annotation')",
"gencode_annotation$species <- 'human'",
"gencode_annotation$version <- '42'",
"getData(gencode_annotation, outdir = 'data/folder', notes = c('gencode', 'annotation', 'human', '42'))",
"",
"## Get data from local catch",
"dataUpdate('data/folder')",
"dataSearch(c('gencode', 'annotation', 'human', '42'))",
"",
"## Get data from Google bucket directly",
"dataUpdate('data/folder', cloud=TRUE)",
"dh <- dataSearch(c('gencode', 'annotation'))",
"getCloudData(dh[1], outdir = 'data/folder')",
sep="\n"))
)
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