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")
strandedness_report = FileField(label="Strandedness report file")
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")
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 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 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."""
report = FileField(label="Bisulfite conversion rate report")
class Output:
"""Output parameters."""
file = FileField(label="File")
class Input:
"""Input parameters."""
src = FileField(label="Input file")
class Output:
"""Output fields."""
bedpe = FileField(label="BEDPE file")
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output fields to process SlamdunkAllPaired."""
tcount = FileField(label="Count report containing SLAMSeq statistics")
species = StringField(label="Species")
build = StringField(label="Build")
class Input:
input_file = FileField(label='Input file', required=True)
class Output:
"""Output parameters."""
bedpe = FileField(label='BEDPE file')
species = StringField(label='Species')
build = StringField(label='Build')
class Output:
"""Output fields for CollectWgsMetrics."""
report = FileField(label="WGS metrics report")
species = StringField(label="Species")
build = StringField(label="Build")
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,
)
class Input:
"""Input fields."""
src = FileField(label="Input file")
class Output:
output_file = FileField(label='Output file')
class Output:
"""Input fields."""
dst = FileField(label="Output file")
class Output:
"""Output fields for AlignmentSummary."""
report = FileField(label="Alignement metrics")
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output fields."""
bigwig = FileField(label="bigwig file")
species = StringField(label="Species")
build = StringField(label="Build")
class Output:
"""Output field of the process UploadProteomicsData."""
table = FileField(label="Uploaded table")
species = StringField(label="Species")
source = StringField(label="Source")
class Output:
"""Output fields."""
plot = FileField(label="QC multiplot")
summary = FileField(label="QC summary")
qorts_data = FileField(label="QoRTs report data")
class Output:
"""Output fields."""
report = FileField(label="Samtools idxstats report")
