Mercurial > repos > galaxyp > data_manager_custom
changeset 0:3c2c36beddb1 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/data_manager_customProDB commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author | galaxyp |
---|---|
date | Fri, 15 Jan 2016 15:52:56 -0500 |
parents | |
children | |
files | data_manager/customProDB_annotation.R data_manager/customProDB_annotation.xml data_manager_conf.xml |
diffstat | 3 files changed, 122 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/customProDB_annotation.R Fri Jan 15 15:52:56 2016 -0500 @@ -0,0 +1,69 @@ +#!/usr/bin/env Rscript + +initial.options <- commandArgs(trailingOnly = FALSE) +script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)])) + +## begin warning handler +withCallingHandlers({ + +library(methods) # Because Rscript does not always do this + +options('useFancyQuotes' = FALSE) + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("RGalaxy")) + + +option_list <- list() +option_list$dbkey <- make_option('--dbkey', type='character') +option_list$outputFile <- make_option('--outputFile', type='character') + +opt <- parse_args(OptionParser(option_list=option_list)) + + +customProDB_annotation <- function( + dbkey = GalaxyCharacterParam(required=TRUE), + outputFile = GalaxyOutput("output","json")) +{ + if (file.exists(outputFile)) + { + if (file.info(outputFile)$size > 0) { gstop("output file already exists") } + else + { + tryCatch( + { + file.remove(outputFile) + }, error=function(err) + { + gstop("failed to remove empty existing file") + }) + } + } + + gstop("what you talkin bout willis?!") +} + + +params <- list() +for(param in names(opt)) +{ + if (!param == "help") + params[param] <- opt[param] +} + +setClass("GalaxyRemoteError", contains="character") +wrappedFunction <- function(f) +{ + tryCatch(do.call(f, params), + error=function(e) new("GalaxyRemoteError", conditionMessage(e))) +} + + +suppressPackageStartupMessages(library(RGalaxy)) +do.call(customProDB_annotation, params) + +## end warning handler +}, warning = function(w) { + cat(paste("Warning:", conditionMessage(w), "\n")) + invokeRestart("muffleWarning") +})
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/customProDB_annotation.xml Fri Jan 15 15:52:56 2016 -0500 @@ -0,0 +1,31 @@ +<tool id="custom_pro_db_annotation_data_manager" name="CustomProDB Annotation" tool_type="manage_data" version="0.0.1"> + <description>builder</description> + <command interpreter="Rscript --vanilla">customProDB_annotation.R + --outputFile "${out_file}" + --dbkey "${dbkey}" + 2>&1 + </command> + <stdio> + <exit_code range=":-1" /> + <exit_code range="1:" /> + </stdio> + <inputs> + <!--<param name="all_fasta_source" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + <param type="text" name="sequence_name" value="" label="Name of sequence" /> + <param type="text" name="sequence_id" value="" label="ID for sequence" />--> + <param type="text" name="dbkey" value="" label="UCSC dbKey for reference genome" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json"/> + </outputs> + + <help> + +.. class:: infomark + +**Notice:** If you leave name, description, or id blank, it will be generated automatically. + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Fri Jan 15 15:52:56 2016 -0500 @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<data_managers> + + <data_manager tool_file="data_manager/customProDB_annotation.xml" id="customProDB_annotation_builder" version="0.0.1"> + <data_table name="customProDB"> + <output> + <column name="value" /> + <column name="dbkey" /> + <column name="name" /> + <column name="path" output_ref="out_file" > + <move type="directory" relativize_symlinks="True"> + <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base --> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/customProDB/${value}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/customProDB/${value}/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> + +</data_managers>