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 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:
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 ChipQC."""
report_folder = DirField(label="ChipQC report folder")
ccplot = FileField(label="Cross coverage score plot")
coverage_histogram = FileField(label="SSD metric plot")
peak_profile = FileField(label="Peak profile plot")
peaks_barplot = FileField(label="Barplot of reads in peaks")
peaks_density_plot = FileField(label="Density plot of reads in peaks")
enrichment_heatmap = FileField(
label="Heatmap of reads in genomic features", required=False)
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output fields to process MergeData"""
file_out = FileField(
label="Labels are short and do not end in a period")
dir_optional = DirField(
label="Labels are short and do not end in a period",
required=False)
list_out = ListField(
FileField(),
label="Labels are short and do not end in a period",
description="Description ends in a period.",
)
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."""
report = FileHtmlField(label="MultiQC report")
report_data = DirField(label="Report data")
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,
)