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")