class Output:
"""Output fields."""
fastq = ListField(FileField(), label='Reverse complemented FASTQ file')
fastq2 = ListField(FileField(), label='Remaining mate')
fastqc_url = ListField(FileHtmlField(), label='Quality control with FastQC (Mate 1)')
fastqc_archive = ListField(FileField(), label='Download FastQC archive (Mate 1)')
fastqc_url2 = ListField(FileHtmlField(), label='Quality control with FastQC (Mate 2)')
fastqc_archive2 = ListField(FileField(), label='Download FastQC archive (Mate 2)')
class Output:
"""Output fields to process ImportScRNA10x."""
barcodes = ListField(FileField(), label='Barcodes')
reads = ListField(FileField(), label='Reads')
fastqc_url_barcodes = ListField(
FileHtmlField(),
label='Quality control with FastQC (Barcodes)',
)
fastqc_url_reads = ListField(
FileHtmlField(),
label='Quality control with FastQC (Reads)',
)
class Output:
"""Output fields for BamToFastqPaired."""
fastq = ListField(FileField(), label="Remaining mate1 reads")
fastq2 = ListField(FileField(), label="Remaining mate2 reads")
fastqc_url = ListField(FileHtmlField(),
label="Mate1 quality control with FastQC")
fastqc_url2 = ListField(FileHtmlField(),
label="Mate2 quality control with FastQC")
fastqc_archive = ListField(FileField(),
label="Download mate1 FastQC archive")
fastqc_archive2 = ListField(FileField(),
label="Download mate2 FastQC archive")
class Output:
"""Output fields."""
fastq = ListField(FileField(), label="Remaining mate 1 reads")
fastq2 = ListField(FileField(), label="Remaining mate 2 reads")
report = FileField(label="Trim galore report", required=False)
fastqc_url = ListField(FileHtmlField(),
label="Mate 1 quality control with FastQC")
fastqc_url2 = ListField(FileHtmlField(),
label="Mate 2 quality control with FastQC")
fastqc_archive = ListField(FileField(),
label="Download mate 1 FastQC archive")
fastqc_archive2 = ListField(FileField(),
label="Download mate 2 FastQC archive")
class Output:
"""Output fields."""
fastq = ListField(FileField(), label='Remaining mate1 reads')
fastq2 = ListField(FileField(), label='Remaining mate2 reads')
report = FileField(label='Cutadapt report')
fastqc_url = ListField(FileHtmlField(),
label='Mate1 quality control with FastQC')
fastqc_url2 = ListField(FileHtmlField(),
label='Mate2 quality control with FastQC')
fastqc_archive = ListField(FileField(),
label='Download mate1 FastQC archive')
fastqc_archive2 = ListField(FileField(),
label='Download mate2 FastQC archive')
class Output:
"""Output fields."""
fastq = ListField(FileField(), label='Reads file.')
report = FileField(label='Cutadapt report')
fastqc_url = ListField(FileHtmlField(), label='Quality control with FastQC.')
fastqc_archive = ListField(FileField(), label='Download FastQC archive.')
class Output:
"""Output fields to process MergeFastqPaired."""
fastq = ListField(FileField(), label="Reads file (mate 1)")
fastq2 = ListField(FileField(), label="Reads file (mate 2)")
fastqc_url = ListField(
FileHtmlField(),
label="Quality control with FastQC (mate 1)",
)
fastqc_url2 = ListField(
FileHtmlField(),
label="Quality control with FastQC (mate 2)",
)
fastqc_archive = ListField(FileField(),
label="Download FastQC archive (mate 1)")
fastqc_archive2 = ListField(FileField(),
label="Download FastQC archive (mate 2)")
class Output:
"""Output fields."""
fastq = ListField(FileField(), label="Reverse complemented FASTQ file")
fastqc_url = ListField(FileHtmlField(),
label="Quality control with FastQC")
fastqc_archive = ListField(FileField(),
label="Download FastQC archive")
class Output:
"""Output fields to process ImportSraSingle."""
fastq = ListField(FileField(), label="Reads file")
fastqc_url = ListField(
FileHtmlField(),
label="Quality control with FastQC",
)
fastqc_archive = ListField(FileField(), label="Download FastQC archive")
class Output:
"""Output fields."""
fastq = ListField(FileField(), label="Reads file")
report = FileField(label="Cutadapt report")
fastqc_url = ListField(FileHtmlField(),
label="Quality control with FastQC")
fastqc_archive = ListField(FileField(),
label="Download FastQC archive")
class Output:
"""Output fields to process ImportScRNA10x."""
matrix_filtered = FileField(label="Matrix (filtered)")
genes_filtered = FileField(label="Genes (filtered)")
barcodes_filtered = FileField(label="Barcodes (filtered)")
matrix_raw = FileField(label="Matrix (raw)")
genes_raw = FileField(label="Genes (raw)")
barcodes_raw = FileField(label="Barcodes (raw)")
report = FileHtmlField(label="Report")
build = StringField(label="Build")
species = StringField(label="Species")
source = StringField(label="Gene ID source")
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,
)