w4mkmeans: w4mkmeans_wrapper.R comparison

comparison w4mkmeans_wrapper.R @ 2:c415b7dc6f37 draft default tip

planemo upload for repository https://github.com/HegemanLab/w4mkmeans_galaxy_wrapper/tree/master commit 3e916537da6bb37e6f3927d7a11e98e0ab6ef5ec

author	eschen42
date	Mon, 05 Mar 2018 12:40:17 -0500
parents	02cafb660b72
children

comparison

equal deleted inserted replaced

-:02cafb660b72
+:c415b7dc6f37
 #     sample_metadata_path "$sampleMetadata_in" \
 #     scores_out "$scores_out" \
 #     slots "${GALAXY_SLOTS:-1}" \
 #     variableMetadata_out "$variableMetadata_out" \
 #     variable_metadata_path "$variableMetadata_in"
 #
 # <inputs>
 #   <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
 #   <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
 #   <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
 #   <param name="categoricalPrefix" label="prefix for cluster names " type="text" value="k" help="Some tools require non-numeric values to discern categorical; e.g., enter 'k' here to prepend 'k' to cluster numbers in the output; default 'k'." />
 #   <param name="kfeatures" label="K value(s) for features" type="text" value="0" help="Single or min,max value(s) for K for features (variables), or 0 for none." />
 #   <param name="ksamples" label="K value(s) for samples" type="text" value="0" help="Single or min,max value(s) for K for samples, or 0 for none." />
-#   <param name="iter_max" label="Max number of iterations" type="text" value="10" help="The maximum number of iterations allowed; default 10." />
+#   <param name="iter_max" label="Max number of iterations" type="text" value="20" help="The maximum number of iterations allowed; default 20." />
-#   <param name="nstart" label="Number of random sets" type="text" value="1" help="How many random sets should be chosen; default 1." />
+#   <param name="nstart" label="Number of random sets" type="text" value="20" help="How many random sets should be chosen; default 20." />
 # 	<param name="algorithm" label="Algorithm for clustering" type="select" value = "Hartigan-Wong" help="K-means clustering algorithm, default 'Hartigan-Wong'; alternatives 'Lloyd', 'MacQueen'; 'Forgy' is a synonym for 'Lloyd', see stats::kmeans reference for further info and references.">
 # 	  <option value="Hartigan-Wong" selected="TRUE">Hartigan-Wong</option>
 # 	  <option value="Lloyd">Lloyd</option>
 # 	  <option value="MacQueen">MacQueen</option>
 # 	  <option value="Forgy">Forgy</option>
 ##----------------------------------------------------------
 ## Computation - source general and module-specific routines
 ##----------------------------------------------------------
 log_print <- function(x, ...) {
 cat(
 format(Sys.time(), "%Y-%m-%dT%H:%M:%S%z")
 , " "
 , c(x, ...)
 , "\n"
 , sep=""
 , file=stderr()
 )
 }
+log_cat <- function(x, ...) {
+cat(
+c(x, ...)
+, "\n"
+, sep=""
+, file=stderr()
+)
+}
 # log_print(sprintf("tool_directory is %s", tool_directory))
 w4m_general_purpose_routines_path <- r_path("w4m_general_purpose_routines.R")
 # log_print(sprintf("w4m_general_purpose_routines_path is %s", w4m_general_purpose_routines_path))
 if ( ! file.exists(w4m_general_purpose_routines_path) ) {
 log_print("cannot find file w4m_general_purpose_routines.R")
 q(save = "no", status = 1, runLast = TRUE)
 }
-# log_print("sourcing ",w4m_general_purpose_routines_path)
+log_print("sourcing ",w4m_general_purpose_routines_path)
 source(w4m_general_purpose_routines_path)
 if ( ! exists("prepare.data.matrix") ) {
 log_print("'prepare.data.matrix' was not read from file w4m_general_purpose_routines.R")
 q(save = "no", status = 1, runLast = TRUE)
 }
 kind_string <- "none"
 tryCatch(
 expr = {
 # read in the sample metadata
 kind_string <- "sample metadata input"
 smpl_metadata_input_env <-
 read_data_frame(
 file_path = env$sample_metadata_path
 , kind_string = kind_string
 , failure_action = failure_action
 )
 }
 env$sampleMetadata <- smpl_metadata_input_env$data
 # read in the variable metadata
 kind_string <- "variable metadata input"
 vrbl_metadata_input_env <-
 read_data_frame(
 file_path = env$variable_metadata_path
 , kind_string = kind_string
 , failure_action = failure_action
 )
 )
 return ( TRUE )
 }
 read_input_failure_action <- function(x, ...) {
 log_print("Failure reading input for '", modNamC, "' Galaxy module call")
 log_print(x, ...)
 }
 ##--------------------------
 ## options
 ##--------
 # Set the handler for R error-handling
 options( show.error.messages = F
 , error = function () {
 log_print( "Fatal error in '", modNamC, "': ", geterrmessage() )
 q( "no", 1, F )
 }
 , warn = -1
 )
 scores_out                      <- as.character(argVc["scores_out"])
 ## input files
 args_env$data_matrix_path       <- as.character(argVc["data_matrix_path"])
 args_env$variable_metadata_path <- as.character(argVc["variable_metadata_path"])
 args_env$sample_metadata_path   <- as.character(argVc["sample_metadata_path"])
 # other parameters
 # multi-string args - split csv: "1,2,3" -> c("1","2","3")
 args_env$kfeatures <- strsplit(x = as.character(argVc['kfeatures']), split = ",", fixed = TRUE)[[1]]
 args_env$ksamples  <- strsplit(x = as.character(argVc['ksamples' ]), split = ",", fixed = TRUE)[[1]]
 log_print("PARAMETERS (parsed):")
 for (member in ls(args_env)) {
 value <- get(member, args_env)
 value <- ifelse(length(value) == 1, value, sprintf("c(%s)", paste(value, collapse=", ")))
 log_print(sprintf("  - %s: %s", member, ifelse( !is.function(value) , value, "function" )))
 }
 log_print("")
 ##---------------------------------------------------------
-## Computation - attempt to read input data
+## Computation - attempt to read input data and process
 ##---------------------------------------------------------
 if ( ! read_input_data(args_env, failure_action = read_input_failure_action) ) {
 result <- -1
 } else {
-log_print("Input data was read successfully.")
+log_print("Input data was read.")
+# attempt to process the data
 result <- w4mkmeans(env = args_env)
-log_print("returned from call to w4mkmeans.")
+log_print("Returned from call to w4mkmeans.")
 }
 if ( length(result) == 0 ) {
 log_print("no results were produced")
 # exit with status code non-zero to indicate error
 ##--------
 ## Closing
 ##--------
 if (!file.exists(sampleMetadata_out)) {
 log_print(sprintf("ERROR %s::w4m_kmeans_wrapper - file '%s' was not created", modNamC, sampleMetadata_out))
 }
 if (!file.exists(variableMetadata_out)) {

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comparison w4mkmeans_wrapper.R @ 2:c415b7dc6f37 draft default tip