class Output:
"""Output fields to process SlamCount."""
exp = FileField(label="Normalized expression")
exp_json = JsonField(label="Expression (json)")
exp_type = StringField(label="Expression type")
rc = FileField(label="T>C read counts")
exp_set = FileField(label="Expressions")
exp_set_json = JsonField(label="Expressions (json)")
source = StringField(label="Gene ID source")
species = StringField(label="Species")
build = StringField(label="Build")
feature_type = StringField(label="Feature type")
class Output:
"""Output fields."""
exp = FileField(label="Normalized expression")
exp_json = JsonField(label="Expression (json)")
exp_type = StringField(label="Expression type")
platform = StringField(label="Microarray platform type")
platform_id = StringField(label="GEO platform ID", required=False)
exp_set = FileField(label="Expressions")
exp_set_json = JsonField(label="Expressions (json)")
source = StringField(label="Gene ID source")
species = StringField(label="Species")
build = StringField(label="Build")
feature_type = StringField(label="Feature type")
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 Output:
"""Output fields."""
exp = FileField(label="Normalized expression")
exp_json = JsonField(label="Expression (json)")
exp_type = StringField(label="Expression type")
rc = FileField(label="Read counts", required=False)
exp_set = FileField(label="Expressions")
exp_set_json = JsonField(label="Expressions (json)")
abundance = FileField(label='StringTie abundance file')
transcripts = FileField(label='StringTie transcripts GTF file')
ctab = FileField(label='StringTie transcripts ctab file')
source = StringField(label="Gene ID source")
species = StringField(label="Species")
build = StringField(label="Build")
feature_type = StringField(label="Feature type")
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 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."""
exp = FileField(label="Normalized expression")
exp_json = JsonField(label="Expression (json)")
exp_type = StringField(label="Expression type")
rc = FileField(label="Read counts", required=False)
exp_set = FileField(label="Expressions")
exp_set_json = JsonField(label="Expressions (json)")
quant = FileField(label="Salmon quant file")
transcripts = FileField(label="Transcript-level expressions")
salmon_output = DirField(label='Salmon output')
txdb = FileField(label="Transcript to gene mapping")
strandedness = StringField(label='Strandedness code')
source = StringField(label="Gene ID source")
species = StringField(label="Species")
build = StringField(label="Build")
feature_type = StringField(label="Feature type")
class Output:
"""Output fields of the process EdgeR."""
raw = FileField("Differential expression")
de_json = JsonField(label="Results table (JSON)")
de_file = FileField(label="Results table (file)")
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 ImportFastaNucleotide."""
all_enhancers = FileField(label="All enhancers table")
enhancers_with_super = FileField(label="Super enhancers table")
plot_points = FileField(label="Plot points")
plot_panel = FileField(label="Plot panel")
enhancer_gene = FileField(label="Enhancer to gene")
enhancer_top_gene = FileField(label="Enhancer to top gene")
gene_enhancer = FileField(label="Gene to Enhancer")
stitch_parameter = FileField(label="Stitch parameter", required=False)
all_output = FileField(label="All output")
scatter_plot = JsonField(label="Super-Enhancer plot")
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output fields of the process Cuffdiff."""
raw = FileField("Differential expression")
de_json = JsonField(label="Results table (JSON)")
de_file = FileField(label="Results table (file)")
transcript_diff_exp = FileField(
label="Differential expression (transcript level)")
tss_group_diff_exp = FileField(
label="Differential expression (primary transcript)")
cds_diff_exp = FileField(
label="Differential expression (coding sequence)")
cuffdiff_output = FileField(label="Cuffdiff output")
source = StringField(label="Gene ID database")
species = StringField(label="Species")
build = StringField(label="Build")
feature_type = StringField(label="Feature type")
class Output:
output_string = JsonField(label="Output string")
output_file = JsonField(label="Output file")
class Input:
"""Input fields to process MergeData."""
string_field = StringField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
choices=[
("computer_readable1", "Human readable 1"),
("computer_readable2", "Human readable 2"),
],
default="computer_readable1",
required=False,
hidden=False,
allow_custom_choice=True,
)
text_field = TextField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
default="default text",
required=False,
hidden=True,
)
boolean_field1 = BooleanField(
label="Labels are short and do not end in a period",
description="Note that description fields always end in a period.",
default=False,
required=True,
hidden=False,
)
integer_field = IntegerField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
default=1,
)
float_field = FloatField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
default=3.14,
)
date_field = DateField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
default="2020-04-20",
)
datetime_field = DateTimeField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
default="2020-04-20 12:16:00",
)
url_field = UrlField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
)
secret_field = SecretField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
)
file_field = FileField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
)
filehtml_field = FileHtmlField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
)
dir_field = DirField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
)
json_field = JsonField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
)
list_field = ListField(
DataField(data_type="your:data:type"),
label="Labels are short and do not end in a period",
description="Description ends in a period.",
)
data_field = DataField(
# data_type should not start with data:
data_type="your:data:type",
label="Labels are short and do not end in a period",
description="Description ends in a period.",
)
class Advanced:
"""Add advanced list of options."""
boolean_field2 = BooleanField(
label="Labels are short and do not end in a period",
description="Description ends in a period.",
default=False,
)
group_field = GroupField(
Advanced,
label="Labels are short and do not end in a period",
disabled=False,
# Will show when boolean_field1 is flipped.
hidden="!boolean_field1",
collapsed=True,
)
