class Input: """Input fields to process MicroarrayExpression.""" exp_unmapped = DataField( "microarray:normalized", label="Unmapped normalized expressions", description= "Unmapped normalized expression with the original probe IDs.", ) exp = FileField( label="Normalized and mapped expressions file", description= "Files should have two columns one with GeneIDs and the other one with expression values." "Expected column names are 'Gene' and 'Expression'.Supported file extensions are .tab.*, .tsv.*, .txt.*", ) source = StringField( label="Gene ID source", allow_custom_choice=True, choices=[ ("AFFY", "AFFY"), ("DICTYBASE", "DICTYBASE"), ("ENSEMBL", "ENSEMBL"), ("NCBI", "NCBI"), ("UCSC", "UCSC"), ], ) build = StringField(label="Genome build", ) 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 Input: """Input fields to process ClusterTimeCourse.""" expressions = ListField( DataField("expression"), relation_type="series", label="Time series relation", description= "Select time course to which the expressions belong to.", ) genes = ListField( StringField(), label="Gene subset", required=False, description="Select at least two genes or leave this field empty.", ) gene_species = StringField( label="Species", description="Species to which the selected genes belong to. " "This field is required if gene subset is set.", required=False, hidden="!genes", allow_custom_choice=True, choices=[ ("Dictyostelium discoideum", "Dictyostelium discoideum"), ("H**o sapiens", "H**o sapiens"), ("Macaca mulatta", "Macaca mulatta"), ("Mus musculus", "Mus musculus"), ("Rattus norvegicus", "Rattus norvegicus"), ], ) gene_source = StringField( label="Gene ID database of selected genes", description="This field is required if gene subset is set.", required=False, hidden="!genes", ) distance = StringField( label="Distance metric", choices=[ ("spearman", "Spearman"), ("pearson", "Pearson"), ], default="spearman", ) linkage = StringField( label="Linkage method", choices=[ ("single", "single"), ("average", "average"), ("complete", "complete"), ], default="average", ) ordering = BooleanField( label="Use optimal ordering", description="Results in a more intuitive tree structure, " "but may slow down the clustering on large datasets", default=False, )
class Output: """Output fields for InsertSizeMetrics.""" report = FileField(label="Insert size metrics") plot = FileField(label="Insert size histogram") species = StringField(label="Species") build = StringField(label="Build")
class Input: """Input fields to process MapMicroarrayProbes.""" expressions = ListField( DataField("microarray:normalized"), label="Normalized expressions", ) mapping_file = FileField( label="File with probe ID mappings", description= "The file should be tab-separated and contain two columns with their column names. The first " "column should contain Gene IDs and the second one should contain probe names. Supported file extensions " "are .tab.*, .tsv.*, .txt.*", required=False, ) source = StringField( label="Gene ID source", description= "Gene ID source used for probe mapping is required when using a custom file.", allow_custom_choice=True, required=False, choices=[ ("AFFY", "AFFY"), ("DICTYBASE", "DICTYBASE"), ("ENSEMBL", "ENSEMBL"), ("NCBI", "NCBI"), ("UCSC", "UCSC"), ], ) build = StringField( label="Genome build", description= "Genome build of mapping file is required when using a custom file.", required=False, )
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 field of the process UploadProteomicsData.""" red_channel = FileField(label="Red channel IDAT file") green_channel = FileField(label="Green channel IDAT file") species = StringField(label="Species") platform = StringField(label="Platform")
class Output: """Output fields for VariantFiltrationVqsr.""" vcf = FileField(label="GVCF file") tbi = FileField(label="Tabix index") species = StringField(label="Species") build = StringField(label="Build")
class Input: """Input fields to process ImportFastaNucleotide.""" src = FileField(label="Sequence file (FASTA)") species = StringField( label="Species", description="Select a species name from the dropdown menu " "or write a custom species name in the species " "field. For sequences that are not related to " "any particular species (e.g. adapters file), " "you can select the value Other.", allow_custom_choice=True, choices=[ ("H**o sapiens", "H**o sapiens"), ("Mus musculus", "Mus musculus"), ("Rattus norvegicus", "Rattus norvegicus"), ("Macaca mulatta", "Macaca mulatta"), ("Dictyostelium discoideum", "Dictyostelium discoideum"), ("Other", "Other"), ], ) build = StringField( label="Genome build", description="Enter a genome build information associated " "with the uploaded sequence(s).", )
class Input: """Input field to process UploadIdatData.""" red_channel = FileField(label="Red channel IDAT file (*_Red.idat)") green_channel = FileField(label="Green channel IDAT file (*_Grn.idat)") species = StringField( label="Species", description="Select a species name from the dropdown menu.", default="H**o sapiens", choices=[ ("H**o sapiens", "H**o sapiens"), ("Mus musculus", "Mus musculus"), ], ) platform = StringField( label="Protein ID database source", description="Select a methylation array platform for human " "(HM450, HM27, EPIC) or mouse (MM285) samples.", default="HM450", choices=[ ("HM450", "HM450"), ("HM27", "HM27"), ("EPIC", "EPIC"), ("MM285", "MM285"), ], )
class Input: """Input fields to process ImportMicroarrayExpression.""" exp = FileField( label="Normalized expression", description= "Normalized expression file with the original probe IDs. Supported file extensions are " ".tab.*, .tsv.*, .txt.*", ) exp_type = StringField(label="Normalization type", ) platform = StringField(label="Microarray platform name", ) platform_id = StringField( label="GEO platform ID", description= "Platform ID according to the GEO database. This can be used in following steps to " "automatically map probe IDs to genes.", required=False, ) species = StringField( label="Species", description= "Select a species name from the dropdown menu or write a custom species name in the species " "field", allow_custom_choice=True, choices=[ ("H**o sapiens", "H**o sapiens"), ("Mus musculus", "Mus musculus"), ("Rattus norvegicus", "Rattus norvegicus"), ("Macaca mulatta", "Macaca mulatta"), ("Dictyostelium discoideum", "Dictyostelium discoideum"), ], )
class Output: """Output fields to process MethylationArraySesame.""" methylation_data = FileField(label="A gzipped tab delimited file (txt.gz)") qc_data = FileField(label="Quality control information from SeSAMe analysis") species = StringField(label="Species") platform = StringField(label="Platform used in the analysis")
class Output: """Output fields for GatkHaplotypeCallerGvcf.""" vcf = FileField(label="GVCF file") tbi = FileField(label="Tabix index") species = StringField(label="Species") build = StringField(label="Build")
class Output: """Output fields to process Import ScBam.""" bam = FileField(label='Uploaded BAM') bai = FileField(label='Index BAI') stats = FileField(label='Alignment statistics') build = StringField(label="Build") species = StringField(label="Species")
class Output: """Output fields for CollectRrbsMetrics.""" report = FileField(label="RRBS summary metrics") detailed_report = FileField(label="Detailed RRBS report") plot = FileField(label="QC plots") species = StringField(label="Species") build = StringField(label="Build")
class Output: """Output fields to process ImportMicroarrayExpression.""" exp = FileField(label="Uploaded normalized expression") exp_type = StringField(label="Normalization type") platform = StringField(label="Microarray platform type") platform_id = StringField(label="GEO platform ID", required=False) species = StringField(label="Species")
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 to process AlleyoopRates.""" report = FileField( label="Tab-separated file containing the overall conversion rates") plot = FileField(label="Overall conversion rate plot file") species = StringField(label="Species") build = StringField(label="Build")
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 UploadOrangeMetadata.""" table = FileField(label="Uploaded table") n_samples = IntegerField(label="Number of samples") features = StringField(label="Number of features") target = StringField(label="Target class description") n_metas = IntegerField(label="Number of meta attributes")
class Output: """Output fields to process MapMicroarrayProbes.""" mapped_exp = FileField(label="Mapped expressions") probe_mapping = StringField(label="Probe to transcript mapping used") mapping = FileField(label="Mapping file") platform = StringField(label="Microarray platform type") platform_id = StringField(label="GEO platform ID", required=False)
class Output: """Output fields to process WgsPreprocess.""" bam = FileField(label="Analysis ready BAM file") bai = FileField(label="BAM file index") stats = FileField(label="Alignment statistics") species = StringField(label="Species") build = StringField(label="Build") metrics_file = FileField(label="Metrics from MarkDuplicate process")
class Output: """Output fields to process AlleyoopSnpEval.""" report = FileField( label="Tab-separated file with read counts, T>C read counts and SNP indication" ) plot = FileField(label="SNP evaluation plot") 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 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: """Output fields to process Bamclipper.""" bam = FileField(label='Clipped BAM file') bai = FileField(label='Index of clipped BAM file') stats = FileField(label='Alignment statistics') bigwig = FileField(label='BigWig file') species = StringField(label='Species') build = StringField(label='Build')
class Output: """Output fields to process Bamclipper.""" bam = FileField(label="Clipped BAM file") bai = FileField(label="Index of clipped BAM file") stats = FileField(label="Alignment statistics") bigwig = FileField(label="BigWig file", required=False) species = StringField(label="Species") build = StringField(label="Build")
class Output: """Output field of the process ImportFastaNucleotide.""" fastagz = FileField(label="FASTA file (compressed)") fasta = FileField(label="FASTA file") fai = FileField(label="FASTA file index") fasta_dict = FileField(label="FASTA dictionary") num_seqs = IntegerField(label="Number of sequences") species = StringField(label="Species") build = StringField(label="Build")
class MyGroup: foo = IntegerField(label="Foo") bar = StringField(label="Bar") group_optional_no_default = StringField( label="Group optional no default", required=False) class SubGroup: foo = IntegerField(label="Foo", default=2) subgroup = GroupField(SubGroup, label="Subgroup")
class Output: """Output fields to process AlleyoopUtrRates.""" report = FileField( label= "Tab-separated file containing conversion rates on each region of interest" ) plot = FileField(label="Region of interest conversion rate plot") species = StringField(label="Species") build = StringField(label="Build")