class OWgcloud_download(OWBwBWidget):
name = "gcloud_download"
description = "Download google bucket files to a local directory"
priority = 5
icon = getIconName(__file__, "gcloud_download.png")
want_main_area = False
docker_image_name = "biodepot/gcp-public-download"
docker_image_tag = "277.0.0__alpine__b2a30b94"
inputs = [("Trigger", str, "handleInputsTrigger"),
("bucket", str, "handleInputsbucket"),
("downloadDir", str, "handleInputsdownloadDir")]
outputs = [("downloadDir", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
bucket = pset("myBucket")
downloadDir = pset("/data")
dirs = pset([])
files = pset([])
noClobber = pset(True)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "gcloud_download")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsbucket(self, value, *args):
if args and len(args) > 0:
self.handleInputs("bucket", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsdownloadDir(self, value, *args):
if args and len(args) > 0:
self.handleInputs("downloadDir",
value,
args[0][0],
test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "downloadDir"):
outputValue = getattr(self, "downloadDir")
self.send("downloadDir", outputValue)
class OWbaserecalibrate(OWBwBWidget):
name = "baserecalibrate"
description = "Base quality recalibration using GATK"
priority = 40
icon = getIconName(__file__,"gatk-bsqr.png")
want_main_area = False
docker_image_name = "biodepot/gatk3-co-clean"
docker_image_tag = "3.6__804cb988"
inputs = [("inputfiles",str,"handleInputsinputfiles"),("reference",str,"handleInputsreference"),("reference_trigger",str,"handleInputsreference_trigger"),("snps_trigger",str,"handleInputssnps_trigger"),("output",str,"handleInputsoutput")]
outputs = [("output",str)]
pset=functools.partial(settings.Setting,schema_only=True)
runMode=pset(0)
exportGraphics=pset(False)
runTriggers=pset([])
triggerReady=pset({})
inputConnectionsStore=pset({})
optionsChecked=pset({})
reference=pset(None)
known=pset(None)
inputfiles=pset([])
output=pset([])
nct=pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__,"baserecalibrate")) as f:
self.data=jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputfiles(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputfiles", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsreference(self, value, *args):
if args and len(args) > 0:
self.handleInputs("reference", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsreference_trigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("reference_trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputssnps_trigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("snps_trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsoutput(self, value, *args):
if args and len(args) > 0:
self.handleInputs("output", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue=None
if hasattr(self,"output"):
outputValue=getattr(self,"output")
self.send("output", outputValue)
class OWText_Output(OWBwBWidget):
name = "Text_Output"
description = "Enter and output a file"
priority = 10
icon = getIconName(__file__, "file.png")
want_main_area = False
docker_image_name = "text-output"
docker_image_tag = "test"
inputs = [("varDir", str, "handleInputsvarDir")]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
varDir = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "Text_Output")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsvarDir(self, value, *args):
if args and len(args) > 0:
self.handleInputs("varDir", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
class OWbwa_index(OWBwBWidget):
name = "bwa_index"
description = "Aligns paired-end sequences, sort and return bam files"
priority = 30
icon = getIconName(__file__, "bwasamsort.png")
want_main_area = False
docker_image_name = "biodepot/bwa-samtools-gdc"
docker_image_tag = "0.7.15__1.9.52__alpine_3.12__da70fa5a"
inputs = [("reference", str, "handleInputsreference"),
("overwrite", str, "handleInputsoverwrite"),
("reference_trigger", str, "handleInputsreference_trigger")]
outputs = [("reference", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
reference = pset(None)
prefix = pset(None)
blocksize = pset(10000000)
algorithm = pset("rb2")
overwrite = pset(True)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "bwa_index")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsreference(self, value, *args):
if args and len(args) > 0:
self.handleInputs("reference", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsoverwrite(self, value, *args):
if args and len(args) > 0:
self.handleInputs("overwrite", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsreference_trigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("reference_trigger",
value,
args[0][0],
test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "reference"):
outputValue = getattr(self, "reference")
self.send("reference", outputValue)
class OWDtoxSAlignment(OWBwBWidget):
name = "DtoxSAlignment"
description = "Alignment part of DtoxS standard operating procedure (SOP)"
priority = 1
icon = getIconName(__file__, "dtoxs-alignment2.svg")
want_main_area = False
docker_image_name = "biodepot/dtoxs_alignment"
docker_image_tag = "1.0__alpine-3.7__bwa-0.715-r1140__python-2.7.14__072818"
inputs = [("barcodesFile", str, "handleInputsbarcodesFile"),
("topDir", str, "handleInputstopDir"),
("trigger", str, "handleInputstrigger")]
outputs = [("topDir", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
topDir = pset(None)
barcodesFile = pset("barcodes_trugrade_96_set4.dat")
lanes = pset(6)
seriesName = pset("20150409")
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "DtoxSAlignment")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsbarcodesFile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("barcodesFile",
value,
args[0][0],
test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputstopDir(self, value, *args):
if args and len(args) > 0:
self.handleInputs("topDir", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputstrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "topDir"):
outputValue = getattr(self, "topDir")
self.send("topDir", outputValue)
class OWmuse_call(OWBwBWidget):
name = "muse_call"
description = "Muse variant caller"
priority = 60
icon = getIconName(__file__, "muse.png")
want_main_area = False
docker_image_name = "biodepot/muse"
docker_image_tag = "1.0rc__alpine_3.13.2__104430b8"
inputs = [("inputfiles", str, "handleInputsinputfiles"),
("reference", str, "handleInputsreference"),
("outputfile", str, "handleInputsoutputfile")]
outputs = [("outputfile", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
reference = pset(None)
region = pset(None)
regionlist = pset(None)
outputfile = pset([])
inputfiles = pset([])
reverse = pset(False)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "muse_call")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputfiles(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputfiles", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsreference(self, value, *args):
if args and len(args) > 0:
self.handleInputs("reference", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsoutputfile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("outputfile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "outputfile"):
outputValue = getattr(self, "outputfile")
self.send("outputfile", outputValue)
class OWpindel_config(OWBwBWidget):
name = "pindel_config"
description = "Generates pindel bam config file"
priority = 72
icon = getIconName(__file__, "pindel.png")
want_main_area = False
docker_image_name = "biodepot/pindel-gdc"
docker_image_tag = "0.2.5b8__10f065ec"
inputs = [("inputfiles", str, "handleInputsinputfiles"),
("Trigger", str, "handleInputsTrigger"),
("configuration", str, "handleInputsconfiguration")]
outputs = [("configuration", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
inputfiles = pset([])
configuration = pset([])
filetags = pset([])
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "pindel_config")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputfiles(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputfiles", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsconfiguration(self, value, *args):
if args and len(args) > 0:
self.handleInputs("configuration",
value,
args[0][0],
test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "configuration"):
outputValue = getattr(self, "configuration")
self.send("configuration", outputValue)
class OWdownloadURL(OWBwBWidget):
name = "downloadURL"
description = "Downloads files from URL"
priority = 6
icon = getIconName(__file__, "download.png")
want_main_area = False
docker_image_name = "biodepot/downloadurl"
docker_image_tag = "alpine_3.13.2__b2680386"
inputs = [("directory", str, "handleInputsdirectory"),
("trigger", str, "handleInputstrigger"),
("URL", str, "handleInputsURL")]
outputs = [("directory", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
URL = pset([])
decompress = pset(True)
directory = pset(None)
concatenateFile = pset(None)
noClobber = pset(False)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "downloadURL")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsdirectory(self, value, *args):
if args and len(args) > 0:
self.handleInputs("directory", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputstrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsURL(self, value, *args):
if args and len(args) > 0:
self.handleInputs("URL", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = "/data"
if hasattr(self, "directory"):
outputValue = getattr(self, "directory")
self.send("directory", outputValue)
class OWgatk_genotypeGVCFs(OWBwBWidget):
name = "gatk_genotypeGVCFs"
description = "Perform joint genotyping on one or more samples pre-called with HaplotypeCaller"
priority = 40
icon = getIconName(__file__,"gatk-genotype-gvcf.png")
want_main_area = False
docker_image_name = "biodepot/gatk"
docker_image_tag = "4.1.9.0__f5684bf4"
inputs = [("inputfile",str,"handleInputsinputfile"),("reference",str,"handleInputsreference"),("reference_trigger",str,"handleInputsreference_trigger"),("output",str,"handleInputsoutput")]
outputs = [("output",str)]
pset=functools.partial(settings.Setting,schema_only=True)
runMode=pset(0)
exportGraphics=pset(False)
runTriggers=pset([])
triggerReady=pset({})
inputConnectionsStore=pset({})
optionsChecked=pset({})
reference=pset(None)
inputfile=pset(None)
output=pset([])
alleles=pset([])
annotateNum=pset(False)
annotation=pset([])
annotationgroup=pset([])
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__,"gatk_genotypeGVCFs")) as f:
self.data=jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputfile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputfile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsreference(self, value, *args):
if args and len(args) > 0:
self.handleInputs("reference", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsreference_trigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("reference_trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsoutput(self, value, *args):
if args and len(args) > 0:
self.handleInputs("output", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue=None
if hasattr(self,"output"):
outputValue=getattr(self,"output")
self.send("output", outputValue)
class OWpindel_biosamba(OWBwBWidget):
name = "pindel_biosamba"
description = "Filters unmapped, duplicate, secondary_alignment, failed_quality_control and supplementary alignments"
priority = 70
icon = getIconName(__file__,"pindel.png")
want_main_area = False
docker_image_name = "biodepot/pindel-gdc"
docker_image_tag = "0.2.5b8__10f065ec"
inputs = [("inputfiles",str,"handleInputsinputfiles"),("Trigger",str,"handleInputsTrigger"),("outputfiles",str,"handleInputsoutputfiles"),("nthreads",str,"handleInputsnthreads")]
outputs = [("outputfiles",str)]
pset=functools.partial(settings.Setting,schema_only=True)
runMode=pset(0)
exportGraphics=pset(False)
runTriggers=pset([])
triggerReady=pset({})
inputConnectionsStore=pset({})
optionsChecked=pset({})
inputfiles=pset([])
outputfiles=pset([])
filter=pset(None)
fileformat=pset(None)
nthreads=pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__,"pindel_biosamba")) as f:
self.data=jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputfiles(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputfiles", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsoutputfiles(self, value, *args):
if args and len(args) > 0:
self.handleInputs("outputfiles", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsnthreads(self, value, *args):
if args and len(args) > 0:
self.handleInputs("nthreads", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue=None
if hasattr(self,"outputfiles"):
outputValue=getattr(self,"outputfiles")
self.send("outputfiles", outputValue)
class OWstarIndex(OWBwBWidget):
name = "starIndex"
description = "Construct indices for STAR aligner "
priority = 11
icon = getIconName(__file__, "starIndex.png")
want_main_area = False
docker_image_name = "biodepot/star"
docker_image_tag = "2.6.0c__debian-8.11-slim__072918"
inputs = [("Trigger", str, "handleInputsTrigger")]
outputs = [("genomeDir", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
rmode = pset("genomeGenerate")
genomeDir = pset(None)
genomeFastaFiles = pset([])
genomeChrBinNbits = pset("18")
genomeSAindexNbases = pset(14)
genomeSAsparseD = pset(1)
genomeSuffixLengthMax = pset(-1)
runThreadN = pset(1)
sjdbGTFfile = pset(None)
sjdbFileChrStartEnd = pset([])
sjdbGTFchrPrefix = pset("chr")
sjdbGTFfeatureExon = pset("exon")
sjdbGTFtagExonParentTranscript = pset("transcript_id")
sjdbGTFtagExonParentGene = pset("gene_id")
sjdbOverhang = pset(100)
sjdbScore = pset(2)
sjdbInsertSave = pset("Basic")
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "starIndex")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None)
def handleOutputs(self):
outputValue = None
if hasattr(self, "genomeDir"):
outputValue = getattr(self, "genomeDir")
self.send("genomeDir", outputValue)
class OWdeseq2(OWBwBWidget):
name = "deseq2"
description = "Differential expression using DESeq2 package"
priority = 14
icon = getIconName(__file__, "deseq2.png")
want_main_area = False
docker_image_name = "biodepot/deseq2"
docker_image_tag = "1.20__ubuntu-16.04__bioc-3.7__r-3.5.1__072918"
inputs = [
("Trigger", str, "handleInputsTrigger"),
("countsFile", str, "handleInputscountsFile"),
]
outputs = [("topGenesFile", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
countsFile = pset(None)
descriptionFile = pset(None)
control = pset(None)
treatment = pset(None)
outputDir = pset(None)
ngenes = pset(50)
topGenesFile = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "deseq2")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None)
def handleInputscountsFile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("countsFile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None)
def handleOutputs(self):
outputValue = None
if hasattr(self, "topGenesFile"):
outputValue = getattr(self, "topGenesFile")
self.send("topGenesFile", outputValue)
class OWsleuth(OWBwBWidget):
name = "sleuth"
description = "Analysis of kallisto quantified RNA-seq files"
priority = 5
icon = getIconName(__file__, "sleuth2.png")
want_main_area = False
docker_image_name = "biodepot/sleuth"
docker_image_tag = "0.30.0__ubuntu-18.04__r-3.5.1__demo__082318"
inputs = [("trigger", str, "handleInputstrigger")]
outputs = [("output_file", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
experimental_description = pset(None)
full_model = pset(None)
filter_fun = pset(None)
norm_fun_counts = pset(None)
norm_fun_tpm = pset(None)
aggregation_column = pset("ext_gene")
transformation_function = pset(None)
num_cores = pset(1)
read_bootstrap_tpm = pset(False)
extra_bootstrap_summary = pset(False)
column = pset(None)
wald = pset(False)
nTopGenes = pset(40)
output_file = pset(None)
qvalue = pset(0.05)
geneNamesFile = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "sleuth")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputstrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None)
def handleOutputs(self):
outputValue = None
if hasattr(self, "output_file"):
outputValue = getattr(self, "output_file")
self.send("output_file", outputValue)
class OWsamtools_index(OWBwBWidget):
name = "samtools_index"
description = "Enter and output a file"
priority = 10
icon = getIconName(__file__, "samindex.png")
want_main_area = False
docker_image_name = "biodepot/samtools"
docker_image_tag = "1.11__alpine_3.12.1__e148c1f4"
inputs = [("inputfile", str, "handleInputsinputfile"),
("outputfile", str, "handleInputsoutputfile")]
outputs = [("inputfile", str), ("outputfile", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
inputfile = pset(None)
outputfile = pset(None)
createcsi = pset(False)
intervalsize = pset(None)
nthreads = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "samtools_index")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputfile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputfile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsoutputfile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("outputfile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "inputfile"):
outputValue = getattr(self, "inputfile")
self.send("inputfile", outputValue)
outputValue = None
if hasattr(self, "outputfile"):
outputValue = getattr(self, "outputfile")
self.send("outputfile", outputValue)
class OWrsem(OWBwBWidget):
name = "rsem"
description = "Rsem"
priority = 1
icon = getIconName(__file__,"rsem.png")
want_main_area = False
docker_image_name = "quay.io/ucsc_cgl/rsem"
docker_image_tag = "1.2.25--d4275175cc8df36967db460b06337a14f40d2f21"
inputs = [("RsemIndexDir",str,"handleInputsRsemIndexDir"),("BamFile",str,"handleInputsBamFile"),("Trigger",str,"handleInputsTrigger")]
outputs = [("OutputDir",str)]
pset=functools.partial(settings.Setting,schema_only=True)
runMode=pset(0)
exportGraphics=pset(False)
runTriggers=pset([])
triggerReady=pset({})
inputConnectionsStore=pset({})
optionsChecked=pset({})
PairedEnd=pset(None)
NoQualities=pset(None)
Threads=pset(None)
ForwardProb=pset(None)
SeedLength=pset(None)
FragmentLengthMean=pset(None)
Bam=pset(None)
ReferencePrefix=pset(None)
OutputPrefix=pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__,"rsem")) as f:
self.data=jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsRsemIndexDir(self, value, *args):
if args and len(args) > 0:
self.handleInputs("RsemIndexDir", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsBamFile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("BamFile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue=None
if hasattr(self,"OutputDir"):
outputValue=getattr(self,"OutputDir")
self.send("OutputDir", outputValue)
class OWgatk_db_import(OWBwBWidget):
name = "gatk_db_import"
description = "Import single-sample GVCFs into GenomicsDB before joint genotyping."
priority = 40
icon = getIconName(__file__, "gatk-db-import.png")
want_main_area = False
docker_image_name = "biodepot/gatk"
docker_image_tag = "4.1.9.0__f5684bf4"
inputs = [("inputfiles", str, "handleInputsinputfiles"),
("output", str, "handleInputsoutput")]
outputs = [("output", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
inputfiles = pset([])
output = pset(None)
annotationgroup = pset([])
regions = pset(None)
readerthreads = pset(1)
overwrite = pset(False)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "gatk_db_import")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputfiles(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputfiles", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsoutput(self, value, *args):
if args and len(args) > 0:
self.handleInputs("output", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "output"):
outputValue = getattr(self, "output")
self.send("output", outputValue)
class OWvs_mpileup(OWBwBWidget):
name = "vs_mpileup"
description = "Samtools mpileup"
priority = 55
icon = getIconName(__file__,"varscan.png")
want_main_area = False
docker_image_name = "biodepot/varscan-samtools"
docker_image_tag = "2.3.9__1.12__jdk-15.0.1_9-alpine"
inputs = [("inputfiles",str,"handleInputsinputfiles"),("reference",str,"handleInputsreference"),("output",str,"handleInputsoutput")]
outputs = [("output",str)]
pset=functools.partial(settings.Setting,schema_only=True)
runMode=pset(0)
exportGraphics=pset(False)
runTriggers=pset([])
triggerReady=pset({})
inputConnectionsStore=pset({})
optionsChecked=pset({})
reference=pset(None)
minmapq=pset(None)
nobaq=pset(False)
inputfiles=pset([])
output=pset([])
reverse=pset(False)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__,"vs_mpileup")) as f:
self.data=jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputfiles(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputfiles", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsreference(self, value, *args):
if args and len(args) > 0:
self.handleInputs("reference", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsoutput(self, value, *args):
if args and len(args) > 0:
self.handleInputs("output", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue=None
if hasattr(self,"output"):
outputValue=getattr(self,"output")
self.send("output", outputValue)
class OWstartodeseq2(OWBwBWidget):
name = "startodeseq2"
description = "Convert Star quantMode counts file to DESeq2 style counts file"
priority = 13
icon = getIconName(__file__, "startodeseq2.png")
want_main_area = False
docker_image_name = "biodepot/star2deseq"
docker_image_tag = "1.0__alpine-3.7__07-29-18"
inputs = [
("inputDirs", str, "handleInputsinputDirs"),
("Trigger", str, "handleInputsTrigger"),
]
outputs = [("outputFile", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
outputFile = pset(None)
inputFile = pset("ReadsPerGene.out.tab")
column = pset(4)
inputDirs = pset([])
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "startodeseq2")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputDirs(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputDirs", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None)
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None)
def handleOutputs(self):
outputValue = None
if hasattr(self, "outputFile"):
outputValue = getattr(self, "outputFile")
self.send("outputFile", outputValue)
class OWbonito(OWBwBWidget):
name = "bonito"
description = "Bonito basecaller"
priority = 8
icon = getIconName(__file__, "bonito.png")
want_main_area = False
docker_image_name = "bonito-cpu"
docker_image_tag = "0.3.8"
inputs = [("modelName", str, "handleInputsmodelName"),
("readsDirectory", str, "handleInputsreadsDirectory")]
outputs = [("OutputFile", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
OutputFile = pset(None)
InputDir = pset(None)
ModelName = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "bonito")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsmodelName(self, value, *args):
if args and len(args) > 0:
self.handleInputs("modelName", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsreadsDirectory(self, value, *args):
if args and len(args) > 0:
self.handleInputs("readsDirectory",
value,
args[0][0],
test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "OutputFile"):
outputValue = getattr(self, "OutputFile")
self.send("OutputFile", outputValue)
class OWStay_Integrator(OWBwBWidget):
name = "Stay_Integrator"
description = "None"
priority = 10
icon = getIconName(__file__, "jigsaw.png")
want_main_area = False
docker_image_name = "uwthinklab/maw_containers_1"
docker_image_tag = "v2"
inputs = [("InputGPS", str, "handleInputsInputGPS"),
("InputCell", str, "handleInputsInputCell")]
outputs = [("Output", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
InputGPS = pset("/data/trans_data/case1_output.csv")
InputCell = pset("/data/trans_data/case2_output.csv")
Output = pset("/data/trans_data/Integrated_results.csv")
DurationConstraint = pset("100")
SpatialConstraint = pset("0.2")
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "Stay_Integrator")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsInputGPS(self, value, *args):
if args and len(args) > 0:
self.handleInputs("InputGPS", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsInputCell(self, value, *args):
if args and len(args) > 0:
self.handleInputs("InputCell", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "Output"):
outputValue = getattr(self, "Output")
self.send("Output", outputValue)
class OWgzip(OWBwBWidget):
name = "gzip"
description = "GunZip"
priority = 1
icon = getIconName(__file__, "compress.png")
want_main_area = False
docker_image_name = "varikmp/gzip"
docker_image_tag = "latest"
inputs = [("FastQCompressedFile", str, "handleInputsFastQCompressedFile"),
("Trigger", str, "handleInputsTrigger")]
outputs = [("FastQPairedFiles", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
HeadSampleFile = pset(None)
TailSampleFile = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "gzip")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsFastQCompressedFile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("FastQCompressedFile",
value,
args[0][0],
test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "FastQPairedFiles"):
outputValue = getattr(self, "FastQPairedFiles")
self.send("FastQPairedFiles", outputValue)
class OWLongshot(OWBwBWidget):
name = "Longshot"
description = "Longshot"
priority = 9
icon = getIconName(__file__,"espresso.png")
want_main_area = False
docker_image_name = "longshot"
docker_image_tag = "0.3.5"
inputs = [("inputFile",str,"handleInputsinputFile"),("inputGenome",str,"handleInputsinputGenome"),("inputRegion",str,"handleInputsinputRegion")]
outputs = [("outputFile",str)]
pset=functools.partial(settings.Setting,schema_only=True)
runMode=pset(0)
exportGraphics=pset(False)
runTriggers=pset([])
triggerReady=pset({})
inputConnectionsStore=pset({})
optionsChecked=pset({})
InputFile=pset(None)
InputGenome=pset(None)
OutputFile=pset(None)
InputRegion=pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__,"Longshot")) as f:
self.data=jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputFile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputFile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsinputGenome(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputGenome", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsinputRegion(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputRegion", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue=None
if hasattr(self,"outputFile"):
outputValue=getattr(self,"outputFile")
self.send("outputFile", outputValue)
class OWStart(OWBwBWidget):
name = "Start"
description = "Enter workflow parameters and start"
priority = 10
icon = getIconName(__file__, "start.png")
want_main_area = False
docker_image_name = "biodepot/gdc-mrna-start"
docker_image_tag = "alpine_3.12__59b7cb77"
outputs = [("work_dir", str), ("genome_dir", str),
("annotation_file", str), ("geneinfo", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
work_dir = pset(None)
genome_dir = pset(None)
annotation_file = pset(None)
geneinfo = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "Start")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleOutputs(self):
outputValue = None
if hasattr(self, "work_dir"):
outputValue = getattr(self, "work_dir")
self.send("work_dir", outputValue)
outputValue = None
if hasattr(self, "genome_dir"):
outputValue = getattr(self, "genome_dir")
self.send("genome_dir", outputValue)
outputValue = None
if hasattr(self, "annotation_file"):
outputValue = getattr(self, "annotation_file")
self.send("annotation_file", outputValue)
outputValue = None
if hasattr(self, "geneinfo"):
outputValue = getattr(self, "geneinfo")
self.send("geneinfo", outputValue)
class OWbash_utils(OWBwBWidget):
name = "bash_utils"
description = "alpine bash with wget curl gzip bzip2"
priority = 1
icon = getIconName(__file__, "bash.png")
want_main_area = False
docker_image_name = "biodepot/bash-utils"
docker_image_tag = "alpine-3.7__081418"
inputs = [
("inputFile", str, "handleInputsinputFile"),
("Trigger", str, "handleInputsTrigger"),
]
outputs = [("OutputDir", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
InputFile = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "bash_utils")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputFile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputFile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None)
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None)
def handleOutputs(self):
outputValue = None
if hasattr(self, "OutputDir"):
outputValue = getattr(self, "OutputDir")
self.send("OutputDir", outputValue)
class OWSelectUserToDisplay(OWBwBWidget):
name = "SelectUserToDisplay"
description = "Minimum Python3 container with pip"
priority = 10
icon = getIconName(__file__,"counting.svg")
want_main_area = False
docker_image_name = "uwthinklab/maw_visualization"
docker_image_tag = "v1"
inputs = [("input_data_path",str,"handleInputsinput_data_path"),("output_data_path",str,"handleInputsoutput_data_path"),("user_name",str,"handleInputsuser_name")]
outputs = [("Output",str)]
pset=functools.partial(settings.Setting,schema_only=True)
runMode=pset(0)
exportGraphics=pset(False)
runTriggers=pset([])
triggerReady=pset({})
inputConnectionsStore=pset({})
optionsChecked=pset({})
input_data_path=pset("/data/trans_data/case1.csv")
output_data_path=pset("/data/trans_data/case1_output.csv")
user_name=pset("284aa3b586cce58e13a3a9cef9b33fa1b1e7fc8e422faa52e126ad7b3ccc767b")
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__,"SelectUserToDisplay")) as f:
self.data=jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinput_data_path(self, value, *args):
if args and len(args) > 0:
self.handleInputs("input_data_path", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsoutput_data_path(self, value, *args):
if args and len(args) > 0:
self.handleInputs("output_data_path", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsuser_name(self, value, *args):
if args and len(args) > 0:
self.handleInputs("user_name", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue=None
if hasattr(self,"Output"):
outputValue=getattr(self,"Output")
self.send("Output", outputValue)
class OWAnalysis_Jupyter(OWBwBWidget):
name = "Analysis_Jupyter"
description = "Jupyter notebook installation with packages for AML analysis"
priority = 103
icon = getIconName(__file__, "jupyter_image.png")
want_main_area = False
docker_image_name = "aml-analysis-jupyter"
docker_image_tag = "latest"
inputs = [("outputDir", str, "handleInputsoutputDir")]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
startingNotebook = pset(None)
type = pset("notebook")
outputNotebook = pset(None)
debug = pset(False)
generateConfig = pset(False)
autoyes = pset(True)
allowRoot = pset(True)
loglevel = pset("30")
port = pset(8888)
config = pset(None)
transport = pset(None)
keyfile = pset(None)
certfile = pset(None)
clientca = pset(None)
outputDir = pset(None)
browser = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "Analysis_Jupyter")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsoutputDir(self, value, *args):
if args and len(args) > 0:
self.handleInputs("outputDir", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
class OWToil_WDL(OWBwBWidget):
name = "WDL"
description = "Toil WDL"
priority = 1
icon = getIconName(__file__, "wdl.png")
want_main_area = False
docker_image_name = "varikmp/toil"
docker_image_tag = "5.2.0"
inputs = [("inputFile", str, "handleInputsinputFile"),
("Trigger", str, "handleInputsTrigger")]
outputs = [("OutputDir", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
WDL_FILE = pset(None)
JSON_FILE = pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "Toil_WDL")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputFile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputFile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsTrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("Trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = None
if hasattr(self, "OutputDir"):
outputValue = getattr(self, "OutputDir")
self.send("OutputDir", outputValue)
class OWguppySetup(OWBwBWidget):
name = "guppySetup"
description = "Downloads files from URL"
priority = 2
icon = getIconName(__file__, "guppy_build..png")
want_main_area = False
docker_image_name = "biodepot/guppy-setup"
docker_image_tag = "ubuntu_20.04__cuda_11.3__9f4d152a"
inputs = [("gpu_url", str, "handleInputsgpu_url"),
("trigger", str, "handleInputstrigger")]
outputs = [("gpu_url", str)]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
gpu_url = pset(None)
overwrite = pset(False)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "guppySetup")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsgpu_url(self, value, *args):
if args and len(args) > 0:
self.handleInputs("gpu_url", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputstrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue = "/data"
if hasattr(self, "gpu_url"):
outputValue = getattr(self, "gpu_url")
self.send("gpu_url", outputValue)
class OWfastqc(OWBwBWidget):
name = "fastqc"
description = "fastqc"
priority = 25
icon = getIconName(__file__,"fastqc_icon_100.png")
want_main_area = False
docker_image_name = "biodepot/fastqc"
docker_image_tag = "0.11.9__ubuntu_20.04__1d825281"
inputs = [("outputDir",str,"handleInputsoutputDir"),("inputFiles",str,"handleInputsinputFiles"),("trigger",str,"handleInputstrigger")]
outputs = [("outputDir",str)]
pset=functools.partial(settings.Setting,schema_only=True)
runMode=pset(0)
exportGraphics=pset(False)
runTriggers=pset([])
triggerReady=pset({})
inputConnectionsStore=pset({})
optionsChecked=pset({})
inputFiles=pset([])
outputDir=pset(None)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__,"fastqc")) as f:
self.data=jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsoutputDir(self, value, *args):
if args and len(args) > 0:
self.handleInputs("outputDir", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputsinputFiles(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputFiles", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputstrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleOutputs(self):
outputValue=None
if hasattr(self,"outputDir"):
outputValue=getattr(self,"outputDir")
self.send("outputDir", outputValue)
class OWigv(OWBwBWidget):
name = "igv"
description = "Integrative Genomics Viewer"
priority = 15
icon = getIconName(__file__, "igv.png")
want_main_area = False
docker_image_name = "biodepot/igv"
docker_image_tag = "2.9.2__ubuntu_20.04__4b93171f"
inputs = [("inputFile", str, "handleInputsinputFile"),
("trigger", str, "handleInputstrigger")]
pset = functools.partial(settings.Setting, schema_only=True)
runMode = pset(0)
exportGraphics = pset(False)
runTriggers = pset([])
triggerReady = pset({})
inputConnectionsStore = pset({})
optionsChecked = pset({})
inputFile = pset([])
genome = pset("hg38")
batch = pset(None)
autoDetermineRegions = pset(True)
def __init__(self):
super().__init__(self.docker_image_name, self.docker_image_tag)
with open(getJsonName(__file__, "igv")) as f:
self.data = jsonpickle.decode(f.read())
f.close()
self.initVolumes()
self.inputConnections = ConnectionDict(self.inputConnectionsStore)
self.drawGUI()
def handleInputsinputFile(self, value, *args):
if args and len(args) > 0:
self.handleInputs("inputFile", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
def handleInputstrigger(self, value, *args):
if args and len(args) > 0:
self.handleInputs("trigger", value, args[0][0], test=args[0][3])
else:
self.handleInputs("inputFile", value, None, False)
