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 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.""" 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: 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 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.""" 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 Input: """Input fields to process WgsPreprocess.""" reads = DataField("reads:fastq:paired", label="Input sample") ref_seq = DataField("seq:nucleotide", label="Reference sequence") bwa_index = DataField("index:bwa", label="BWA genome index") known_sites = ListField(DataField("variants:vcf"), label="Known sites of variation (VCF)") advanced = BooleanField( label="Show advanced options", description="Inspect and modify parameters.", default=False, ) class AdvancedOptions: """Advanced options.""" pixel_distance = IntegerField( label="--OPTICAL_DUPLICATE_PIXEL_DISTANCE", default=2500, description="Set the optical pixel distance, e.g. " "distance between clusters. Modify this parameter to " "ensure compatibility with older Illumina platforms.", ) advanced_options = GroupField(AdvancedOptions, label="Advanced options", hidden="!advanced")
class Input: """Input fields to process MergeFastqSingle.""" reads = ListField( DataField(data_type="reads:fastq:single:"), label="Reads data objects", )
class Input: """Input fields to process ImportSra.""" sra_accession = ListField(StringField(), label="SRA accession(s)") show_advanced = BooleanField(label="Show advanced options", default=False) class Advanced: """Advanced options.""" prefetch = BooleanField(label="Prefetch SRA file", default=True) max_size_prefetch = StringField( label="Maximum file size to download in KB", default="20G", description="A unit prefix can be used instead of a value in KB (e.g. 1024M or 1G).", ) min_spot_id = IntegerField(label="Minimum spot ID", required=False) max_spot_id = IntegerField(label="Maximum spot ID", required=False) min_read_len = IntegerField(label="Minimum read length", required=False) clip = BooleanField(label="Clip adapter sequences", default=False) aligned = BooleanField(label="Dump only aligned sequences", default=False) unaligned = BooleanField( label="Dump only unaligned sequences", default=False ) advanced = GroupField( Advanced, label="Advanced options", hidden="!show_advanced" )
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 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 Input: """Input fields to process MergeFastqPaired.""" reads = ListField( DataField(data_type="reads:fastq:paired:"), label="Reads data objects", )
class Input: """Input fields to process ImportScRNA10x.""" barcodes = ListField( FileField( description= 'Barcodes file(s) in FASTQ format. Usually the forward FASTQ files (R1).', ), label='Barcodes (.fastq.gz)', ) reads = ListField( FileField( description= 'Reads file(s) in FASTQ format. Usually the reverse FASTQ files (R2).', ), label='Reads (.fastq.gz)', )
class Input: """Input fields for GatkGenotypeGVCFs.""" gvcfs = ListField( DataField("variants:gvcf"), label="Input data (GVCF)", ) ref_seq = DataField("seq:nucleotide", label="Reference sequence") intervals = DataField( "bed", label="Intervals file (.bed)", ) dbsnp = DataField("variants:vcf", label="dbSNP file") advanced = BooleanField( label="Show advanced options", description="Inspect and modify parameters.", default=False, ) class AdvancedOptions: """Advanced options.""" batch_size = IntegerField( label="Batch size", default=0, description="Batch size controls the number of samples " "for which readers are open at once and therefore provides " "a way to minimize memory consumption. However, it can " "take longer to complete. Use the consolidate flag if more " "than a hundred batches were used. This will improve feature " "read time. batchSize=0 means no batching " "(i.e. readers for all samples will be opened at once).", ) consolidate = BooleanField( label="Consolidate", default=False, description="Boolean flag to enable consolidation. If " "importing data in batches, a new fragment is created for " "each batch. In case thousands of fragments are created, " "GenomicsDB feature readers will try to open ~20x as many " "files. Also, internally GenomicsDB would consume more " "memory to maintain bookkeeping data from all fragments. " "Use this flag to merge all fragments into one. Merging " "can potentially improve read performance, however overall " "benefit might not be noticeable as the top Java layers " "have significantly higher overheads. This flag has no " "effect if only one batch is used.", ) advanced_options = GroupField(AdvancedOptions, label="Advanced options", hidden="!advanced")
class Input: """Input fields for AlleyoopSummary.""" slamdunk = ListField( DataField( data_type="alignment:bam:slamdunk", description="Select one or multiple data objects from slamdunk process.", ), label="Slamdunk results", )
class Input: """Input fields to process MultiQC.""" data = ListField( DataField( data_type="", description= "Select multiple data objects for which the MultiQC report is to be " "generated.", ), label="Input data", ) class Advanced: """Options.""" dirs = BooleanField( label="--dirs", default=True, description="Prepend directory to sample names.", ) dirs_depth = IntegerField( label="--dirs-depth", default=-1, description= "Prepend a specified number of directories to sample names. Enter a " "negative number (default) to take from start of path.", ) fullnames = BooleanField( label="--fullnames", default=False, description= "Disable the sample name cleaning (leave as full file name).", ) config = BooleanField( label="Use configuration file", default=True, description= "Use Genialis configuration file for MultiQC report.", ) cl_config = StringField( label="--cl-config", required=False, description= "Enter text with command-line configuration options to override the " "defaults (e.g. custom_logo_url: https://www.genialis.com).", ) advanced = GroupField(Advanced, label="Advanced options")
class Input: """Input fields to process EdgeR.""" case = ListField( DataField("expression"), label="Case", description="Case samples (replicates)", ) control = ListField( DataField("expression"), label="Control", description="Control samples (replicates)", ) count_filter = IntegerField( label="Raw counts filtering threshold", default=10, description="Filter genes in the expression matrix input. " "Remove genes where the number of counts in all samples is " "below the threshold.", ) create_sets = BooleanField( label="Create gene sets", description="After calculating differential gene " "expressions create gene sets for up-regulated genes, " "down-regulated genes and all genes.", default=False, ) logfc = FloatField( label="Log2 fold change threshold for gene sets", description="Genes above Log2FC are considered as " "up-regulated and genes below -Log2FC as down-regulated.", default=1.0, hidden="!create_sets", ) fdr = FloatField( label="FDR threshold for gene sets", default=0.05, hidden="!create_sets", )
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.""" 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 Input: """Input fields to perform Base quality score recalibration.""" bam = DataField("alignment:bam", label="BAM file containing reads") reference = DataField("seq:nucleotide", label="Reference genome file") known_sites = ListField( DataField( data_type="variants:vcf", description= "One or more databases of known polymorphic sites used to exclude regions around known " "polymorphisms from analysis.", ), label="List of known sites of variation", ) intervals = DataField( data_type="bed", required=False, label="One or more genomic intervals over which to operate.", description= "This field is optional, but it can speed up the process by restricting calculations to " "specific genome regions.", ) read_group = StringField( label="Replace read groups in BAM", description= "Replace read groups in a BAM file.This argument enables the user to replace all read groups " "in the INPUT file with a single new read group and assign all reads to this read group in " "the OUTPUT BAM file. Addition or replacement is performed using Picard's " "AddOrReplaceReadGroups tool. Input should take the form of -name=value delimited by a " '";", e.g. "-ID=1;-LB=GENIALIS;-PL=ILLUMINA;-PU=BARCODE;-SM=SAMPLENAME1". See tool\'s ' "documentation for more information on tag names. Note that PL, LB, PU and SM are require " "fields. See caveats of rewriting read groups in the documentation.", default="", ) validation_stringency = StringField( label="Validation stringency", description= "Validation stringency for all SAM files read by this program. Setting stringency to SILENT " "can improve performance when processing a BAM file in which variable-length data (read, " "qualities, tags) do not otherwise need to be decoded. Default is STRICT. This setting is " "used in BaseRecalibrator and ApplyBQSR processes.", choices=[ ("STRICT", "STRICT"), ("LENIENT", "LENIENT"), ("SILENT", "SILENT"), ], default="STRICT", )
class Input: """Input fields to perform Base quality score recalibration.""" bam = DataField('alignment:bam', label='BAM file containing reads') reference = DataField('genome:fasta', label='Reference genome file') known_sites = ListField( DataField( data_type='variants:vcf', description= 'One or more databases of known polymorphic sites used to exclude regions around known ' 'polymorphisms from analysis.'), label='List of known sites of variation', ) intervals = DataField( data_type='bed', label='One or more genomic intervals over which to operate.', description= 'This field is optional, but it can speed up the process by restricting calculations to ' 'specific genome regions.') read_group = StringField( label='Replace read groups in BAM', description= 'Replace read groups in a BAM file.This argument enables the user to replace all read groups ' 'in the INPUT file with a single new read group and assign all reads to this read group in ' 'the OUTPUT BAM file. Addition or replacement is performed using Picard\'s ' 'AddOrReplaceReadGroups tool. Input should take the form of -name=value delimited by a ' '";", e.g. "-ID=1;-LB=GENIALIS;-PL=ILLUMINA;-PU=BARCODE;-SM=SAMPLENAME1". See tool\'s ' 'documentation for more information on tag names. Note that PL, LB, PU and SM are require ' 'fields. See caveats of rewriting read groups in the documentation.', default='') validation_stringency = StringField( label='Validation stringency', description= 'Validation stringency for all SAM files read by this program. Setting stringency to SILENT ' 'can improve performance when processing a BAM file in which variable-length data (read, ' 'qualities, tags) do not otherwise need to be decoded. Default is STRICT. This setting is ' 'used in BaseRecalibrator and ApplyBQSR processes.', choices=[ ('STRICT', 'STRICT'), ('LENIENT', 'LENIENT'), ('SILENT', 'SILENT'), ], default='STRICT', )
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 Input: """Input fields to process ShortHairpinRNADifferentialExpression.""" parameter_file = DataField( data_type="file", label="Excel parameter file (.xlsx)", description="Select .xlsx file which holds parameters for analysis. " "See [here](https://github.com/genialis/shRNAde/blob/master/inst/extdata/template_doDE_inputs" ".xlsx) for a template.", ) expression_data = ListField( DataField( data_type="expression:shrna2quant:", description= "Data objects of expressions from process shrna-quant. These inputs should match sample " "names specified in parameter file.", ), label="List of expression files from shrna2quant", )
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="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 Input: """Input fields to process FindSimilar.""" expressions = ListField( DataField("expression"), relation_type="series", label="Time series relation", description="Select time course to which the expressions belong to.", ) gene = StringField( label="Query gene", description="Select a gene to which others are compared.", ) distance = StringField( label="Distance metric", choices=[ ("spearman", "Spearman"), ("pearson", "Pearson"), ], default="spearman", )
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 Input: data_name = StringField(label="Data name") sample_name = StringField(label="Collection name") tags = ListField(StringField(), label="My tags")
class Input: """Input fields.""" data = ListField(DataField(data_type=""), label="Data.")