# ---------------------------------------------------------------------------- # Copyright (c) 2023, QIIME 2 development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- from qiime2.core.type import Bool, Choices, Float, Int, List, Range, Str megahit_params = { "presets": Str % Choices(["meta", "meta-sensitive", "meta-large", "disabled"]), "min_count": Int % Range(1, None), "k_list": List[Int % Range(15, 255, inclusive_end=True)], "k_min": Int % Range(15, 255, inclusive_end=True), "k_max": Int % Range(15, 255, inclusive_end=True), "k_step": Int % Range(2, 28, inclusive_end=True), "no_mercy": Bool, "bubble_level": Int % Range(0, 2, inclusive_end=True), "prune_level": Int % Range(0, 3, inclusive_end=True), "prune_depth": Int % Range(1, None), "disconnect_ratio": Float % Range(0, 1, inclusive_end=True), "low_local_ratio": Float % Range(0, 1, inclusive_end=True), "max_tip_len": Int % Range(1, None) | Str % Choices(["auto"]), "cleaning_rounds": Int % Range(1, None), "no_local": Bool, "kmin_1pass": Bool, "memory": Float % Range(0, None), "mem_flag": Int % Range(0, None), "num_cpu_threads": Int % Range(1, None), "no_hw_accel": Bool, "min_contig_len": Int, } # fmt: off megahit_param_descriptions = { "presets": "Override a group of parameters. See the megahit documentation " "for details.", "min_count": "Minimum multiplicity for filtering (k_min+1)-mers.", "k_list": "List of kmer size - all must be odd with an increment <= 28.", "k_min": "Minimum kmer size (<= 255), must be odd number. Overrides k_list.", "k_max": "Maximum kmer size (<= 255), must be odd number. Overrides k_list.", "k_step": "Increment of kmer size of each iteration (<= 28), must be even number. " "Overrides k_list.", "no_mercy": "Do not add mercy kmers.", "bubble_level": "Intensity of bubble merging, 0 to disable.", "prune_level": "Strength of low depth pruning.", "prune_depth": "Remove unitigs with avg kmer depth less than this value.", "disconnect_ratio": "Disconnect unitigs if its depth is less than this ratio times " "the total depth of itself and its siblings.", "low_local_ratio": "Remove unitigs if its depth is less than this ratio times " "the average depth of the neighborhoods.", "max_tip_len": "Remove tips less than this value. 'auto' will trim tips shorter " "than 2*k for iteration of kmer_size=k", "cleaning_rounds": "Number of rounds for graph cleanning.", "no_local": "Disable local assembly.", "kmin_1pass": "Use 1pass mode to build SdBG of k_min.", "memory": "Max memory in byte to be used in SdBG construction (if set between 0-1, " "fraction of the machine's total memory).", "mem_flag": "SdBG builder memory mode. 0: minimum; 1: moderate; " "others: use all memory specified by '-m/--memory'.", "num_cpu_threads": "Number of CPU threads.", "no_hw_accel": "Run MEGAHIT without BMI2 and POPCNT hardware instructions.", "min_contig_len": "Minimum length of contigs to output.", } # fmt: on spades_params = { "isolate": Bool, "sc": Bool, "meta": Bool, "bio": Bool, "corona": Bool, "plasmid": Bool, "metaviral": Bool, "metaplasmid": Bool, "only_assembler": Bool, "careful": Bool, "disable_rr": Bool, "threads": Int % Range(1, None), "memory": Int % Range(1, None), "k": List[Int % Range(1, 128, inclusive_end=False) | Str % Choices(["auto"])], "cov_cutoff": Float % Range(0, 1, inclusive_start=False) | Str % Choices(["auto", "off"]), "phred_offset": Str % Choices(["auto-detect", "33", "64"]), "debug": Bool, } # fmt: off spades_param_descriptions = { "isolate": "This flag is highly recommended for high-coverage isolate and " "multi-cell data.", "sc": "This flag is required for MDA (single-cell) data.", "meta": "This flag is required for metagenomic data.", "bio": "This flag is required for biosyntheticSPAdes mode.", "corona": "This flag is required for coronaSPAdes mode.", "plasmid": "Runs plasmidSPAdes pipeline for plasmid detection.", "metaviral": "Runs metaviralSPAdes pipeline for virus detection.", "metaplasmid": "Runs metaplasmidSPAdes pipeline for plasmid detection in " "metagenomic datasets (equivalent for --meta --plasmid).", "only_assembler": "Runs only assembling (without read error correction).", "careful": "Tries to reduce number of mismatches and short indels.", "disable_rr": "Disables repeat resolution stage of assembling.", "threads": "Number of threads.", "memory": "RAM limit for SPAdes in Gb (terminates if exceeded).", "k": "List of k-mer sizes (must be odd and less than 128).", "cov_cutoff": "Coverage cutoff value (a positive float number, or 'auto', or " "'off').", "phred_offset": "PHRED quality offset in the input reads (33 or 64).", "debug": "Runs SPAdes in debug mode.", } # fmt: on quast_params = { # TODO: add eukaryote, fungal and large when alignment # to reference is supported "min_contig": Int % Range(1, None), "threads": Int % Range(1, None), "k_mer_stats": Bool, "k_mer_size": Int % Range(1, None), "contig_thresholds": List[Int % Range(0, None)], } # fmt: off quast_param_descriptions = { "min_contig": "Lower threshold for contig length.", "threads": "Maximum number of parallel jobs." "Currently supported on Linux only.", "k_mer_stats": "Compute k-mer-based quality metrics (recommended for large " "genomes). This may significantly increase memory and time " "consumption on large genomes.", "k_mer_size": "Size of k used in k-mer-stats.", "contig_thresholds": "List of contig length thresholds.", } # fmt: on iss_params = { "sample_names": List[Str], "n_genomes": Int % Range(1, None), "ncbi": List[Str % Choices(["bacteria", "viruses", "archaea"])], "n_genomes_ncbi": List[Int % Range(1, None)], "abundance": Str % Choices( [ "uniform", "halfnormal", "exponential", "lognormal", "zero-inflated-lognormal", "off", ] ), "coverage": Str % Choices( ["halfnormal", "exponential", "lognormal", "zero-inflated-lognormal", "off"] ), "model": Str % Choices(["HiSeq", "NovaSeq", "MiSeq"]), "n_reads": Int % Range(1, None), "mode": Str % Choices(["kde", "basic", "perfect"]), "gc_bias": Bool, "cpus": Int % Range(1, None), "debug": Bool, "seed": Int % Range(0, None), } # fmt: off iss_param_descriptions = { "sample_names": "List of sample names that should be generated. ", "n_genomes": "How many genomes will be used for the simulation. " "Only required when genome sequences are provided.", "ncbi": "Download input genomes from NCBI. Can be bacteria, viruses, archaea " "or a combination of the three.", "n_genomes_ncbi": "How many genomes will be downloaded from NCBI. If more than " "one kingdom is set with --ncbi, multiple values are necessary.", "abundance": "Abundance distribution.", "coverage": "Coverage distribution.", "model": "Error model. Use either of the precomputed models when --mode " "set to 'kde'.", "n_reads": "Number of reads to generate.", "mode": "Error model. If not specified, using kernel density estimation.", "gc_bias": "If set, may fail to sequence reads with abnormal GC content.", "cpus": "Number of cpus to use.", "debug": " Enable debug logging.", "seed": "Seed for all the random number generators.", } # fmt: on bowtie2_indexing_params = { "large_index": Bool, "debug": Bool, "sanitized": Bool, "verbose": Bool, "noauto": Bool, "packed": Bool, "bmax": Int % Range(1, None) | Str % Choices(["auto"]), "bmaxdivn": Int % Range(1, None), "dcv": Int % Range(1, None), "nodc": Bool, "offrate": Int % Range(0, None), "ftabchars": Int % Range(1, None), "threads": Int % Range(1, None), "seed": Int % Range(0, None), } # fmt: off bowtie2_indexing_param_descriptions = { "large_index": "Force generated index to be 'large', even if ref has " "fewer than 4 billion nucleotides.", "debug": "Use the debug binary; slower, assertions enabled.", "sanitized": "Use sanitized binary; slower, uses ASan and/or UBSan.", "verbose": "Log the issued command.", "noauto": " Disable automatic -p/--bmax/--dcv memory-fitting.", "packed": "Use packed strings internally; slower, less memory.", "bmax": "Max bucket sz for blockwise suffix-array builder.", "bmaxdivn": "Max bucket sz as divisor of ref len.", "dcv": "Diff-cover period for blockwise.", "nodc": "Disable diff-cover (algorithm becomes quadratic).", "offrate": "SA is sampled every 2^ BWT chars.", "ftabchars": "# of chars consumed in initial lookup.", "threads": "# of CPUs.", "seed": "Seed for random number generator.", } # fmt: on bowtie2_mapping_params = { "skip": Int % Range(0, None), "qupto": Int % Range(1, None) | Str % Choices(["unlimited"]), "trim5": Int % Range(0, None), "trim3": Int % Range(0, None), "trim_to": Str, "phred33": Bool, "phred64": Bool, "mode": Str % Choices(["local", "global"]), "sensitivity": Str % Choices(["very-fast", "fast", "sensitive", "very-sensitive"]), "n": Int % Range(0, 1, inclusive_end=True), "len": Int % Range(1, None), "i": Str, "n_ceil": Str, "dpad": Int % Range(0, None), "gbar": Int % Range(0, None), "ignore_quals": Bool, "nofw": Bool, "norc": Bool, "no_1mm_upfront": Bool, "end_to_end": Bool, "local": Bool, "ma": Int % Range(0, None), "mp": Int % Range(0, None), "np": Int % Range(0, None), "rdg": Str, "rfg": Str, "k": Int % Range(0, None) | Str % Choices(["off"]), "a": Bool, "d": Int % Range(0, None), "r": Int % Range(0, None), "minins": Int % Range(0, None), "maxins": Int % Range(1, None), "valid_mate_orientations": Str % Choices(["fr", "rf", "ff"]), "no_mixed": Bool, "no_discordant": Bool, "dovetail": Bool, "no_contain": Bool, "no_overlap": Bool, "offrate": Int % Range(0, None) | Str % Choices(["off"]), "threads": Int % Range(1, None), "reorder": Bool, "mm": Bool, "seed": Int % Range(0, None), "non_deterministic": Bool, } # fmt: off bowtie2_mapping_param_descriptions = { "skip": "Skip (i.e. do not align) the first reads or pairs in the input.", "qupto": "Align the first reads or read pairs from the input (after the " "-s/--skip reads or pairs have been skipped), then stop.", "trim5": "Trim bases from 5' (left) end of each read before alignment.", "trim3": "Trim bases from 3' (right) end of each read before alignment.", "trim_to": "Trim reads exceeding bases. Bases will be trimmed from either " "the 3' (right) or 5' (left) end of the read. If the read end is not " "specified, bowtie2 will default to trimming from the 3' (right) end " "of the read. --trim-to and -trim3/-trim5 are mutually exclusive. " "The value of this parameter should have the following format: " "[3:|5:], e.g.: '5:120' if bases should be trimmed from 3' end or " "just '120' if the end is not specified. Set to 'untrimmed' to perform " "no trimming.", "phred33": 'Input qualities are ASCII chars equal to the Phred quality plus 33, ' 'i.e., "Phred+33" encoding.', "phred64": 'Input qualities are ASCII chars equal to the Phred quality plus 64, ' 'i.e., "Phred+64" encoding.', "mode": "bowtie2 alignment settings. See bowtie2 manual for more details.", "sensitivity": "bowtie2 alignment sensitivity. See bowtie2 manual for details.", "n": "Sets the number of mismatches to allowed in a seed alignment during " "multiseed alignment. Setting this higher makes alignment slower (often much " "slower) but increases sensitivity.", "len": "Sets the length of the seed substrings to align during multiseed " "alignment. Smaller values make alignment slower but more sensitive. " "Default: the --sensitive preset is used by default, which sets -L to " "22 and 20 in --end-to-end mode and in --local mode.", "i": 'Sets a function governing the interval between seed substrings to use during ' 'multiseed alignment. The value of this parameter should be provided as a ' 'comma-separated list, e.g.: "S,1,0.75". For details on how to set functions ' 'consult Bowtie 2 manual.', "n_ceil": 'Sets a function governing the maximum number of ambiguous characters ' '(usually Ns and/or .s) allowed in a read as a function of read length. ' 'The value of this parameter should be provided as a comma-separated ' 'list, e.g.: "L,1,0.75". For details on how to set functions consult ' 'bowtie2 manual.', "dpad": '"Pads" dynamic programming problems by columns on either side to ' 'allow gaps.', "gbar": "Disallow gaps within positions of the beginning or end of the read.", "ignore_quals": "When calculating a mismatch penalty, always consider the quality " "value at the mismatched position to be the highest possible, " "regardless of the actual value. I.e. input is treated as though " "all quality values are doesn't specify quality values (e.g. " "in -f, -r, or -c modes).", "nofw": "If --nofw is specified, bowtie2 will not attempt to align unpaired reads " "to the forward (Watson) reference strand. In paired-end mode, pertains to " "the fragments. For more information, consult the Bowtie 2 manual.", "norc": "If --norc is specified, bowtie2 will not attempt to align unpaired reads " "against the reverse-complement (Crick) reference strand. In paired-end " "mode, pertains to the fragments. For more information, consult the " "bowtie2 manual.", "no_1mm_upfront": "By default, Bowtie 2 will attempt to find either an exact or a " "1-mismatch end-to-end alignment for the read before trying the " "multiseed heuristic. Such alignments can be found very quickly, " "and many short read alignments have exact or near-exact " "end-to-end alignments. However, this can lead to unexpected " "alignments when the user also sets options governing the " "multiseed heuristic, like -L and -N. For instance, if the user " "specifies -N 0 and -L equal to the length of the read, the user " "will be surprised to find 1-mismatch alignments reported. " "This option prevents Bowtie 2 from searching for 1-mismatch " "end-to-endalignments before using the multiseed heuristic, " "which leads to the expected behavior when combined with options " "such as -L and -N. This comes at the expense of speed.", "end_to_end": 'In this mode, Bowtie 2 requires that the entire read align from ' 'one end to the other, without any trimming (or "soft clipping") of ' 'characters from either end. The match bonus --ma always equals 0 in ' 'this mode, so all alignment scores are less than or equal to 0, and ' 'the greatest possible alignment score is 0. This is mutually ' 'exclusive with --local. --end-to-end is the default mode.', "local": 'In this mode, bowtie2 does not require that the entire read align from ' 'one end to the other. Rather, some characters may be omitted ' '("soft clipped") from the ends in order to achieve the greatest possible ' 'alignment score. The match bonus --ma is used in this mode, and the best ' 'possible alignment score is equal to the match bonus (--ma) times the ' 'length of the read. Specifying --local and one of the presets (e.g. ' '--local --very-fast) is equivalent to specifying the local version of ' 'the preset (--very-fast-local). This is mutually exclusive with ' '--end-to-end. --end-to-end is the default mode.', "ma": "Sets the match bonus. In --local mode is added to the alignment score " "for each position where a read character aligns to a reference character " "and the characters match. Not used in --end-to-end mode.", "mp": "max penalty for mismatch; lower qual = lower penalty.", "np": "Sets penalty for positions where the read, reference, or both, contain an " "ambiguous character such as N.", "rdg": "Sets the read gap open () and extend () penalties. A read gap " "of length N gets a penalty of + N * . The value of this " "parameter should be provided as a comma-separated list of two integers.", "rfg": "Sets the reference gap open () and extend () penalties. " "A reference gap of length N gets a penalty of + N * . The " "value of this parameter should be provided as a comma-separated list of " "two integers.", "k": "Report up to alns per read. By default, bowtie2 searches for " "distinct, valid alignments for each read. When it finds a valid alignment, " "it continues looking for alignments that are nearly as good or better. The " "best alignment found is reported (randomly selected from among best if " "tied). Information about the best alignments is used to estimate mapping " "quality and to set SAM optional fields, such as AS:i and XS:i. When -k is " "specified, however, bowtie2 searches for at most distinct, valid " "alignments for each read. The search terminates when it can't find more " "distinct valid alignments, or when it finds , whichever happens first. " "All alignments found are reported in descending order by alignment score. " "For more information, consult the bowtie2 manual.", "a": "Report all alignments. Like -k but with no upper limit on number of " "alignments to search for. -a is mutually exclusive with -k. Note: Bowtie 2 " "is not designed with -a mode in mind, and when aligning reads to long, " "repetitive genomes this mode can be very, very slow.", "d": 'Up to consecutive seed extension attempts can "fail" before bowtie2 ' 'moves on, using the alignments found so far. A seed extension "fails" if it ' 'does not yield a new best or a new second-best alignment. This limit is ' 'automatically adjusted up when -k or -a are specified.', "r": ' is the maximum number of times Bowtie 2 will "re-seed" reads with ' 'repetitive seeds. When "re-seeding," bowtie2 simply chooses a new set of ' 'reads (same length, same number of mismatches allowed) at different offsets ' 'and searches for more alignments. A read is considered to have repetitive ' 'seeds if the total number of seed hits divided by the number of seeds that ' 'aligned at least once is greater than 300.', "minins": "The minimum fragment length for valid paired-end alignments.", "maxins": "The maximum fragment length for valid paired-end alignments.", "valid_mate_orientations": "The upstream/downstream mate orientations for a valid " "paired-end alignment against the forward reference " "strand. For more details consult the bowtie2 manual.", "no_mixed": "By default, when bowtie2 cannot find a concordant or discordant " "alignment for a pair, it then tries to find alignments for the " "individual mates. This option disables that behavior.", "no_discordant": "By default, bowtie2 looks for discordant alignments if it " "cannot find any concordant alignments. This option disables " "that behavior.", "dovetail": 'If the mates "dovetail", that is if one mate alignment extends past ' 'the beginning of the other such that the wrong mate begins upstream, ' 'consider that to be concordant.', "no_contain": "If one mate alignment contains the other, consider that " "to be non-concordant.", "no_overlap": "If one mate alignment overlaps the other at all, consider that " "to be non-concordant.", "offrate": "Override the offrate of the index with . If is greater than " "the offrate used to build the index, then some row markings are " "discarded when the index is read into memory. This reduces the memory " "footprint of the aligner but requires more time to calculate text " "offsets. must be greater than the value used to build the index.", "threads": "Launch > parallel search threads. Threads will run on separate " "processors/cores and synchronize when parsing reads and outputting " "alignments. Searching for alignments is highly parallel, and speedup " "is close to linear. Increasing -p increases Bowtie 2's memory " "footprint.", "reorder": "Guarantees that output SAM records are printed in an order " "corresponding to the order of the reads in the original input file, " "even when --threads is set greater than 1.", "mm": "Use memory-mapped I/O to load the index, rather than typical file I/O. " "Memory-mapping allows many concurrent bowtie processes on the same computer " "to share the same memory image of the index.", "seed": "Use as the seed for pseudo-random number generator.", "non_deterministic": "If specified, Bowtie 2 re-initializes its pseudo-random " "generator for each read using the current time.", } # fmt: on