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| #!/bin/python | |
| import json | |
| import sys | |
| import datetime | |
| import os | |
| #The following python script is designed to take in a directory of json files containing GATK tools, | |
| # and output a WDL task file for each one. | |
| def getWdlType(jsonType): | |
| if(jsonType.lower() == "double"): | |
| return "Float" | |
| elif(jsonType.lower() == "integer" or jsonType.lower() == "int"): | |
| return "Int" | |
| elif(jsonType.lower() == "boolean"): | |
| return "Boolean" | |
| elif(jsonType.lower() == "file"): | |
| return "File" | |
| elif("list" in jsonType.lower()): | |
| substring = jsonType[jsonType.find("[")+1:len(jsonType)-1] | |
| return "Array[" + getWdlType(substring) + "]" | |
| else: | |
| return "String" | |
| def getArgIndexByName(nameStr, args): | |
| for x in range(0,len(args)): | |
| if args[x]["name"].lower() == nameStr.lower(): | |
| return x | |
| return -1 | |
| def checkName(nameStr): | |
| index = nameStr.find(":") | |
| if nameStr =="input": | |
| return checkName("task_" + nameStr) | |
| elif index>0: | |
| return checkName(nameStr[0:index] + nameStr[index+1:]) | |
| else: | |
| return nameStr | |
| def checkQuotes(myStr): | |
| index = myStr.find("\"") | |
| if index < 0: | |
| return myStr | |
| else: | |
| return checkQuotes(myStr[0:index]+myStr[index+1:]) | |
| #collect inputs | |
| directory = sys.argv[1] | |
| version = sys.argv[2] | |
| dirFiles = os.listdir(directory) | |
| engineJson = directory + "/engine_args_per_tool.json" | |
| cmdJson = directory + "/org_broadinstitute_gatk_engine_CommandLineGATK.php.json" | |
| #open files and grab data | |
| with open(engineJson) as engineFile: | |
| engineData = json.load(engineFile) | |
| with open(cmdJson) as cmdFile: | |
| cmdData = json.load(cmdFile) | |
| dirJsons = [] | |
| for a in range(0, len(dirFiles)): | |
| if ".json" in dirFiles[a] and "gatk_tools" in dirFiles[a]: | |
| dirJsons.append(directory + "/" + dirFiles[a]) | |
| #iterate over each file in the directory of jsons | |
| #TODO: change 3 to len(dirJsons) | |
| for a in range(0,len(dirJsons)): | |
| toolJson = dirJsons[a] | |
| #open the tool file, and load the data | |
| with open(toolJson) as toolFile: | |
| toolData = json.load(toolFile) | |
| #grab frequently used sections from toolData for easier access | |
| toolName = toolData["name"] | |
| toolArgs = toolData["arguments"] | |
| cmdArgs = cmdData["arguments"] | |
| if("Tools" in toolData["group"]): | |
| #open the output file | |
| filename = directory + "/WDLTasks/" + toolName + "_" + version + ".wdl" | |
| wdlFile = open(filename, 'w') | |
| #parse the summary text to cut after \n | |
| cutIndex = toolData["summary"].find("\n") | |
| if cutIndex > 0: | |
| toolSummary = toolData["summary"][0:cutIndex] | |
| else: | |
| toolSummary = toolData["summary"] | |
| #Write header and declare task | |
| wdlFile.write("# --------------------------------------------------------------------------------------------\n" + | |
| "# This " + toolName + " WDL task was generated on " + datetime.date.today().strftime("%m/%d/%y") + | |
| " for use with GATK version " + version + "\n" + | |
| "# For more information on using this wrapper, please see the WDL repository at \n" + | |
| "# https://github.com/broadinstitute/wdl/tree/develop/scripts/wrappers/gatk/README.md\n" + | |
| "# Task Summary: " + toolSummary + "\n" + | |
| "# --------------------------------------------------------------------------------------------\n\n") | |
| wdlFile.write("task " + toolName + " { \n") | |
| #declare default inputs | |
| wdlFile.write("\tFile gatk\n" + | |
| "\tFile ref\n" + | |
| "\tFile refIndex\n" + | |
| "\tFile refDict\n" + | |
| "\tString ? userString #If a parameter you'd like to use is missing from this task, use this term to add your own string\n") | |
| #declare engine-level inputs | |
| if toolName in engineData.keys(): | |
| for b in range(0,len(engineData[toolName])): | |
| if engineData[toolName][b][2].lower() == "required": | |
| wdlFile.write("\t" + getWdlType(cmdArgs[getArgIndexByName(engineData[toolName][b][0], cmdArgs)]["type"]) + | |
| " " + checkName(engineData[toolName][b][0][2:]) + "\n") | |
| elif engineData[toolName][b][2].lower() == "optional": | |
| wdlFile.write("\t" + getWdlType(cmdArgs[getArgIndexByName(engineData[toolName][b][0], cmdArgs)]["type"]) + | |
| " ? " + checkName(engineData[toolName][b][0][2:]) + "\n") | |
| else: | |
| print("There was an error determining the optional status of an engine argument: Input received: " | |
| + engineData[toolName][e][2] + " for the argument " + toolName + ": " + engineData[toolName][e][0]) | |
| #iterate through remaining inputs (non-defaults) | |
| for b in range(0,len(toolData["parallel"])): | |
| wdlFile.write("\tInt ? " + toolData["parallel"][b]["arg"][1:] + "Val\n") | |
| for b in range(0,len(toolArgs)): | |
| if toolArgs[b]["required"] == "yes": | |
| wdlFile.write("\t" + getWdlType(toolArgs[b]["type"]) + " " + checkName(toolArgs[b]["name"][2:]) + "\n") | |
| elif toolArgs[b]["required"] == "no": | |
| wdlFile.write("\t" + getWdlType(toolArgs[b]["type"]) + " ? " + checkName(toolArgs[b]["name"][2:]) + "\n") | |
| else: | |
| print("There was an error determining optional status of an argument. Input received: " | |
| + toolArgs[b]["required"] + " for the argument " + toolArgs[b]["synonyms"]) | |
| #write command | |
| wdlFile.write("\n\tcommand {\n" + | |
| "\t\tjava -jar ${gatk} \\\n" + | |
| "\t\t\t-T " + toolName + " \\\n" + | |
| "\t\t\t-R ${ref} \\\n") | |
| #add additional engine-level arguments | |
| if toolName in engineData.keys(): | |
| for b in range(0,len(engineData[toolName])): | |
| if engineData[toolName][b][2].lower() == "required": | |
| wdlFile.write("\t\t\t" + engineData[toolName][b][0] + " ${" + checkName(engineData[toolName][b][0][2:]) + "} \\\n") | |
| elif engineData[toolName][b][2].lower() == "optional": | |
| if engineData[toolName][b][1].lower() == "null": | |
| wdlFile.write("\t\t\t${default=\"\" \"" + engineData[toolName][b][0] + " \" + " + checkName(engineData[toolName][b][0][2:]) + | |
| "} \\\n") | |
| else: | |
| wdlFile.write("\t\t\t" + engineData[toolName][b][0] + " ${default=\"" + checkQuotes(engineData[toolName][b][1]) + "\" " + | |
| checkName(engineData[toolName][b][0][2:]) + "} \\\n") | |
| else: | |
| print("There was an error determining the optional status of an engine argument: Input received: " + | |
| engineData[toolName][b][2] + " for the argument " + toolName + ": " + engineData[toolName][b][0]) | |
| #iterate through remaining options (non-defaults) | |
| for b in range(0,len(toolData["parallel"])): | |
| wdlFile.write("\t\t\t${default=\"\" \"" + toolData["parallel"][b]["arg"] + "\" + " + toolData["parallel"][b]["arg"][1:] + "Val} \\\n") | |
| for b in range(0,len(toolArgs)): | |
| if toolArgs[b]["required"] == "yes": | |
| wdlFile.write("\t\t\t" + toolArgs[b]["synonyms"] + " ${" + checkName(toolArgs[b]["name"][2:]) + "} \\\n") | |
| elif toolArgs[b]["required"] == "no": | |
| if toolArgs[b]["defaultValue"] != "NA" and toolArgs[b]["defaultValue"] != "none" and toolArgs[b]["defaultValue"] != "[ ]": | |
| if toolArgs[b]["synonyms"] != "NA": | |
| wdlFile.write("\t\t\t" + toolArgs[b]["synonyms"] + " ${default=\"" + checkQuotes(toolArgs[b]["defaultValue"]) + "\" " + | |
| checkName(toolArgs[b]["name"][2:]) + "} \\\n") | |
| else: | |
| wdlFile.write("\t\t\t" + checkName(toolArgs[b]["name"][2:]) + " ${default=\"" + checkQuotes(toolArgs[b]["defaultValue"]) + "\" " + | |
| checkName(toolArgs[b]["name"][2:]) + "} \\\n") | |
| else: | |
| if toolArgs[b]["synonyms"] != "NA": | |
| wdlFile.write("\t\t\t${default=\"\" \"" + toolArgs[b]["synonyms"] + " \" + " + checkName(toolArgs[b]["name"][2:]) + "} \\\n") | |
| else: | |
| wdlFile.write("\t\t\t${default=\"\" \"" + checkName(toolArgs[b]["name"][2:]) + " \" + " + checkName(toolArgs[b]["name"][2:]) + "} \\\n") | |
| else: | |
| print("There was an error determining optional status of an argument. Input received: " + | |
| toolArgs[b]["required"] + " for the argument " + toolArgs[b]["synonyms"]) | |
| wdlFile.write("\t\t\t${default=\"\\n\" userString} \n" + | |
| "\t}\n") | |
| #write output | |
| wdlFile.write("\n\toutput {\n" + | |
| "\t\t#To track additional outputs from your task, please manually add them below\n" + | |
| "\t\tString taskOut = \"${out}\"\n" + | |
| "\t}\n") | |
| #write runtime | |
| #TODO Replace docker image with GATK-specific one | |
| wdlFile.write("\n\truntime {\n" + | |
| "\t\tdocker: \"broadinstitute/genomes-in-the-cloud:2.2.2-1466113830\"\n" + | |
| "\t}\n") | |
| #write parameter_meta | |
| wdlFile.write("\n\tparameter_meta {\n" + | |
| "\t\tgatk: \"Executable jar for the GenomeAnalysisTK\"\n" + | |
| "\t\tref: \"fasta file of reference genome\"\n" + | |
| "\t\trefIndex: \"Index file of reference genome\"\n" + | |
| "\t\trefDict: \"dict file of reference genome\"\n" + | |
| "\t\tuserString: \"An optional parameter which allows the user to specify additions to the command line at run time\"\n") | |
| for b in range(0,len(toolArgs)): | |
| wdlFile.write("\t\t" + checkName(toolArgs[b]["name"][2:]) + ": \"" + checkQuotes(toolArgs[b]["summary"]) + "\"\n") | |
| if toolName in engineData.keys(): | |
| for b in range(0,len(engineData[toolName])): | |
| wdlFile.write("\t\t" + checkName(engineData[toolName][b][0][2:]) + ": \"" + | |
| checkQuotes(cmdArgs[getArgIndexByName(engineData[toolName][b][0], cmdArgs)]["summary"]) + "\"\n" ) | |
| wdlFile.write("\t}\n}") | |
| #close file | |
| wdlFile.close() |