class Input:
"""Input fields to process MicroarrayExpression."""
exp_unmapped = DataField(
"microarray:normalized",
label="Unmapped normalized expressions",
description=
"Unmapped normalized expression with the original probe IDs.",
)
exp = FileField(
label="Normalized and mapped expressions file",
description=
"Files should have two columns one with GeneIDs and the other one with expression values."
"Expected column names are 'Gene' and 'Expression'.Supported file extensions are .tab.*, .tsv.*, .txt.*",
)
source = StringField(
label="Gene ID source",
allow_custom_choice=True,
choices=[
("AFFY", "AFFY"),
("DICTYBASE", "DICTYBASE"),
("ENSEMBL", "ENSEMBL"),
("NCBI", "NCBI"),
("UCSC", "UCSC"),
],
)
build = StringField(label="Genome build", )
probe_mapping = StringField(label="Probe to transcript mapping used", )
class Input:
"""Input fields."""
my_field = StringField(label="My field")
my_list = ListField(StringField(), label="My list")
input_data = DataField("test:save", label="My input data")
input_entity_data = DataField("entity", label="My entity data")
bar = DataField(data_type="test:save", label="My bar")
url = UrlField(UrlField.DOWNLOAD, label="My URL")
integer = IntegerField(label="My integer")
my_float = FloatField(label="My float")
my_json = JsonField(label="Blah blah")
my_optional = StringField(label="Optional",
required=False,
default="default value")
my_optional_no_default = StringField(label="Optional no default",
required=False)
class MyGroup:
foo = IntegerField(label="Foo")
bar = StringField(label="Bar")
group_optional_no_default = StringField(
label="Group optional no default", required=False)
my_group = GroupField(MyGroup, label="My group")
class Input:
"""Input fields to process ClusterTimeCourse."""
expressions = ListField(
DataField("expression"),
relation_type="series",
label="Time series relation",
description=
"Select time course to which the expressions belong to.",
)
genes = ListField(
StringField(),
label="Gene subset",
required=False,
description="Select at least two genes or leave this field empty.",
)
gene_species = StringField(
label="Species",
description="Species to which the selected genes belong to. "
"This field is required if gene subset is set.",
required=False,
hidden="!genes",
allow_custom_choice=True,
choices=[
("Dictyostelium discoideum", "Dictyostelium discoideum"),
("H**o sapiens", "H**o sapiens"),
("Macaca mulatta", "Macaca mulatta"),
("Mus musculus", "Mus musculus"),
("Rattus norvegicus", "Rattus norvegicus"),
],
)
gene_source = StringField(
label="Gene ID database of selected genes",
description="This field is required if gene subset is set.",
required=False,
hidden="!genes",
)
distance = StringField(
label="Distance metric",
choices=[
("spearman", "Spearman"),
("pearson", "Pearson"),
],
default="spearman",
)
linkage = StringField(
label="Linkage method",
choices=[
("single", "single"),
("average", "average"),
("complete", "complete"),
],
default="average",
)
ordering = BooleanField(
label="Use optimal ordering",
description="Results in a more intuitive tree structure, "
"but may slow down the clustering on large datasets",
default=False,
)
class Output:
"""Output fields for InsertSizeMetrics."""
report = FileField(label="Insert size metrics")
plot = FileField(label="Insert size histogram")
species = StringField(label="Species")
build = StringField(label="Build")
class Input:
"""Input fields to process MapMicroarrayProbes."""
expressions = ListField(
DataField("microarray:normalized"),
label="Normalized expressions",
)
mapping_file = FileField(
label="File with probe ID mappings",
description=
"The file should be tab-separated and contain two columns with their column names. The first "
"column should contain Gene IDs and the second one should contain probe names. Supported file extensions "
"are .tab.*, .tsv.*, .txt.*",
required=False,
)
source = StringField(
label="Gene ID source",
description=
"Gene ID source used for probe mapping is required when using a custom file.",
allow_custom_choice=True,
required=False,
choices=[
("AFFY", "AFFY"),
("DICTYBASE", "DICTYBASE"),
("ENSEMBL", "ENSEMBL"),
("NCBI", "NCBI"),
("UCSC", "UCSC"),
],
)
build = StringField(
label="Genome build",
description=
"Genome build of mapping file is required when using a custom file.",
required=False,
)
class Output:
"""Output fields to process CellRangerMkref."""
genome_index = DirField(label="Indexed genome")
build = StringField(label="Build")
species = StringField(label="Species")
source = StringField(label="Gene ID source")
class Output:
"""Output field of the process UploadProteomicsData."""
red_channel = FileField(label="Red channel IDAT file")
green_channel = FileField(label="Green channel IDAT file")
species = StringField(label="Species")
platform = StringField(label="Platform")
class Output:
"""Output fields for VariantFiltrationVqsr."""
vcf = FileField(label="GVCF file")
tbi = FileField(label="Tabix index")
species = StringField(label="Species")
build = StringField(label="Build")
class Input:
"""Input fields to process ImportFastaNucleotide."""
src = FileField(label="Sequence file (FASTA)")
species = StringField(
label="Species",
description="Select a species name from the dropdown menu "
"or write a custom species name in the species "
"field. For sequences that are not related to "
"any particular species (e.g. adapters file), "
"you can select the value Other.",
allow_custom_choice=True,
choices=[
("H**o sapiens", "H**o sapiens"),
("Mus musculus", "Mus musculus"),
("Rattus norvegicus", "Rattus norvegicus"),
("Macaca mulatta", "Macaca mulatta"),
("Dictyostelium discoideum", "Dictyostelium discoideum"),
("Other", "Other"),
],
)
build = StringField(
label="Genome build",
description="Enter a genome build information associated "
"with the uploaded sequence(s).",
)
class Input:
"""Input field to process UploadIdatData."""
red_channel = FileField(label="Red channel IDAT file (*_Red.idat)")
green_channel = FileField(label="Green channel IDAT file (*_Grn.idat)")
species = StringField(
label="Species",
description="Select a species name from the dropdown menu.",
default="H**o sapiens",
choices=[
("H**o sapiens", "H**o sapiens"),
("Mus musculus", "Mus musculus"),
],
)
platform = StringField(
label="Protein ID database source",
description="Select a methylation array platform for human "
"(HM450, HM27, EPIC) or mouse (MM285) samples.",
default="HM450",
choices=[
("HM450", "HM450"),
("HM27", "HM27"),
("EPIC", "EPIC"),
("MM285", "MM285"),
],
)
class Input:
"""Input fields to process ImportMicroarrayExpression."""
exp = FileField(
label="Normalized expression",
description=
"Normalized expression file with the original probe IDs. Supported file extensions are "
".tab.*, .tsv.*, .txt.*",
)
exp_type = StringField(label="Normalization type", )
platform = StringField(label="Microarray platform name", )
platform_id = StringField(
label="GEO platform ID",
description=
"Platform ID according to the GEO database. This can be used in following steps to "
"automatically map probe IDs to genes.",
required=False,
)
species = StringField(
label="Species",
description=
"Select a species name from the dropdown menu or write a custom species name in the species "
"field",
allow_custom_choice=True,
choices=[
("H**o sapiens", "H**o sapiens"),
("Mus musculus", "Mus musculus"),
("Rattus norvegicus", "Rattus norvegicus"),
("Macaca mulatta", "Macaca mulatta"),
("Dictyostelium discoideum", "Dictyostelium discoideum"),
],
)
class Output:
"""Output fields to process MethylationArraySesame."""
methylation_data = FileField(label="A gzipped tab delimited file (txt.gz)")
qc_data = FileField(label="Quality control information from SeSAMe analysis")
species = StringField(label="Species")
platform = StringField(label="Platform used in the analysis")
class Output:
"""Output fields for GatkHaplotypeCallerGvcf."""
vcf = FileField(label="GVCF file")
tbi = FileField(label="Tabix index")
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output fields to process Import ScBam."""
bam = FileField(label='Uploaded BAM')
bai = FileField(label='Index BAI')
stats = FileField(label='Alignment statistics')
build = StringField(label="Build")
species = StringField(label="Species")
class Output:
"""Output fields for CollectRrbsMetrics."""
report = FileField(label="RRBS summary metrics")
detailed_report = FileField(label="Detailed RRBS report")
plot = FileField(label="QC plots")
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output fields to process ImportMicroarrayExpression."""
exp = FileField(label="Uploaded normalized expression")
exp_type = StringField(label="Normalization type")
platform = StringField(label="Microarray platform type")
platform_id = StringField(label="GEO platform ID", required=False)
species = StringField(label="Species")
class Output:
"""Output field of the process ClusterTimeCourse."""
cluster = JsonField(label="Hieararhical clustering")
source = StringField(label="Gene ID database")
species = StringField(label="Species")
build = StringField(label="Build")
feature_type = StringField(label="Feature type")
class Output:
"""Output fields to process AlleyoopRates."""
report = FileField(
label="Tab-separated file containing the overall conversion rates")
plot = FileField(label="Overall conversion rate plot file")
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output field of the process FindSimilar."""
similar_genes = JsonField(label="Similar genes")
source = StringField(label="Gene ID database")
species = StringField(label="Species")
build = StringField(label="Build")
feature_type = StringField(label="Feature type")
class Output:
"""Output field of the process UploadOrangeMetadata."""
table = FileField(label="Uploaded table")
n_samples = IntegerField(label="Number of samples")
features = StringField(label="Number of features")
target = StringField(label="Target class description")
n_metas = IntegerField(label="Number of meta attributes")
class Output:
"""Output fields to process MapMicroarrayProbes."""
mapped_exp = FileField(label="Mapped expressions")
probe_mapping = StringField(label="Probe to transcript mapping used")
mapping = FileField(label="Mapping file")
platform = StringField(label="Microarray platform type")
platform_id = StringField(label="GEO platform ID", required=False)
class Output:
"""Output fields to process WgsPreprocess."""
bam = FileField(label="Analysis ready BAM file")
bai = FileField(label="BAM file index")
stats = FileField(label="Alignment statistics")
species = StringField(label="Species")
build = StringField(label="Build")
metrics_file = FileField(label="Metrics from MarkDuplicate process")
class Output:
"""Output fields to process AlleyoopSnpEval."""
report = FileField(
label="Tab-separated file with read counts, T>C read counts and SNP indication"
)
plot = FileField(label="SNP evaluation plot")
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
string_output = StringField(label="My string output")
list_string_output = ListField(StringField(), label="My list string output")
file_output = FileField(label="My output")
list_file_output = ListField(FileField(), label="My list output")
dir_output = DirField(label="My output")
input_data_name = StringField(label="Input data name")
input_entity_name = StringField(label="Input entity name")
docker_image = StringField(label="Docker image")
class Output:
"""Output fields to process BWAIndex."""
index = DirField(label="BWA index")
fastagz = FileField(label="FASTA file (compressed)")
fasta = FileField(label="FASTA file")
fai = FileField(label="FASTA file index")
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output fields to process Bamclipper."""
bam = FileField(label='Clipped BAM file')
bai = FileField(label='Index of clipped BAM file')
stats = FileField(label='Alignment statistics')
bigwig = FileField(label='BigWig file')
species = StringField(label='Species')
build = StringField(label='Build')
class Output:
"""Output fields to process Bamclipper."""
bam = FileField(label="Clipped BAM file")
bai = FileField(label="Index of clipped BAM file")
stats = FileField(label="Alignment statistics")
bigwig = FileField(label="BigWig file", required=False)
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output field of the process ImportFastaNucleotide."""
fastagz = FileField(label="FASTA file (compressed)")
fasta = FileField(label="FASTA file")
fai = FileField(label="FASTA file index")
fasta_dict = FileField(label="FASTA dictionary")
num_seqs = IntegerField(label="Number of sequences")
species = StringField(label="Species")
build = StringField(label="Build")
class MyGroup:
foo = IntegerField(label="Foo")
bar = StringField(label="Bar")
group_optional_no_default = StringField(
label="Group optional no default", required=False)
class SubGroup:
foo = IntegerField(label="Foo", default=2)
subgroup = GroupField(SubGroup, label="Subgroup")
class Output:
"""Output fields to process AlleyoopUtrRates."""
report = FileField(
label=
"Tab-separated file containing conversion rates on each region of interest"
)
plot = FileField(label="Region of interest conversion rate plot")
species = StringField(label="Species")
build = StringField(label="Build")
