miga-base 1.2.15.2 → 1.2.15.4

data/utils/enveomics/Manifest/Tasks/ogs.json

@@ -1,382 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "ogs.annotate.rb",
-      "description": ["Annotates Orthology Groups (OGs) using one or more",
-        "reference genomes."],
-      "see_also": ["ogs.mcl.rb"],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "Input file",
-          "opt": "--in",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Input file containing the OGs (as generated by",
-            "ogs.mcl.rb)."]
-        },
-        {
-          "name": "Output file",
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output file containing the annotated OGs."
-        },
-        {
-          "name": "Annotations",
-          "opt": "-a",
-          "arg": "in_file",
-          "mandatory": true,
-          "multiple_sep": ",",
-          "description": ["Input file(s) containing the annotations. One or",
-            "more tab-delimited files with the gene names in the first column",
-            "and the annotation in the second."]
-        },
-        {
-          "opt": "--format",
-          "arg": "string",
-          "default": "(\\S+)\\.txt",
-          "description": ["Format of the filenames for the annotation files,",
-            "using regex syntax."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "ogs.core-pan.rb",
-      "description": ["Subsamples the genomes in a set of Orthology Groups",
-        "(OGs) and estimates the trend of core genome and pangenome sizes."],
-      "help_arg": "--help",
-      "requires": [
-        {
-          "ruby_gem": "json"
-        }
-      ],
-      "see_also": ["ogs.mcl.rb"],
-      "options": [
-        {
-          "opt": "--ogs",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input file containing the precomputed OGs."
-        },
-        {
-          "opt": "--summary",
-          "arg": "out_file",
-          "description": ["Output file in tabular format with summary",
-            "statistics."]
-        },
-        {
-          "opt": "--tab",
-          "arg": "out_file",
-          "description": "Output file in tabular format."
-        },
-        {
-          "opt": "--json",
-          "arg": "out_file",
-          "description": "Output file in JSON format."
-        },
-        {
-          "opt": "--replicates",
-          "arg": "integer",
-          "description": "Number of replicates to estimate.",
-          "default": 100
-        },
-        {
-          "opt": "--threads",
-          "arg": "integer",
-          "description": "Children threads to spawn."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "ogs.extract.rb",
-      "description": ["Extracts sequences of Orthology Groups (OGs) from",
-        "genomes (proteomes)."],
-      "help_arg": "--help",
-      "see_also": ["ogs.mcl.rb"],
-      "options": [
-        {
-          "name": "Input file",
-          "opt": "--in",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Input file containing the OGs (as generated by",
-            "ogs.mcl.rb)."]
-        },
-        {
-          "name": "Output file",
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output directory where to place extracted sequences."
-        },
-        {
-          "name": "Sequences",
-          "opt": "--seqs",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Path to the proteomes in FastA format, using '%s'",
-            "to denote the genome. For example: /path/to/seqs/%s.faa."]
-        },
-        {
-          "opt": "--core",
-          "arg": "float",
-          "description": ["Use only OGs present in at least this fraction of",
-            "the genomes. To use only the strict core genome*, use --core 1."],
-          "note": ["* To use only the unus genome (OGs with exactly one gene",
-            "per genome), use: --core 1 --duplicates 1."]
-        },
-        {
-          "opt": "--duplicates",
-          "arg": "integer",
-          "description": ["Use only OGs with less than this number of",
-            "in-paralogs in a genome. To use only genes without in-paralogs*,",
-            "use --duplicates 1."],
-          "note": ["* To use only the unus genome (OGs with exactly one gene",
-            "per genome), use: --core 1 --duplicates 1."]
-        },
-        {
-          "opt": "--per-genome",
-          "description": ["If set, the output is generated per genome. By",
-            "default, the output is per OG."]
-        },
-        {
-          "opt": "--prefix",
-          "description": ["If set, each sequence is prefixed with the genome",
-            "name (or OG number, if --per-genome) and a dash."]
-        },
-        {
-          "opt": "--rand",
-          "description": ["Get only one gene per genome per OG (random)",
-            "regardless of in-paralogs. By default all genes are extracted."]
-        },
-        {
-          "opt": "--first",
-          "description": ["Get only one gene per genome per OG (first)",
-            "regardless of in-paralogs. By default all genes are extracted.",
-            "Takes precedence over --rand."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "ogs.mcl.rb",
-      "description": ["Identifies Orthology Groups (OGs) in Reciprocal Best",
-        "Matches (RBM) between all pairs in a collection of genomes, using the",
-        "Markov Cluster Algorithm."],
-      "see_also": ["ogs.annotate.rb", "ogs.core-pan.rb", "ogs.extract.rb",
-        "ogs.stats.rb"],
-      "cite": [["Enright et al, 2002, NAR",
-        "http://dx.doi.org/10.1093/nar/30.7.1575"]],
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output file containing the detected OGs."
-        },
-        {
-          "opt": "--dir",
-          "arg": "in_dir",
-          "description": "Directory containing the RBM files.",
-          "note": "Mandatory, unless --abc is set to a non-empty file."
-        },
-        {
-          "opt": "--format",
-          "arg": "string",
-          "description": ["Format of the filenames for the RBM files (within",
-            "--dir), using regex syntax."],
-          "default": "(\\S+)-(\\S+)\\.rbm"
-        },
-        {
-          "opt": "--inflation",
-          "arg": "float",
-          "description": "Inflation parameter for MCL clustering.",
-          "default": 1.5
-        },
-        {
-          "opt": "--blind",
-          "description": ["If set, computes clusters without taking bitscore",
-            "into account."]
-        },
-        {
-          "opt": "--evalue",
-          "description": ["If set, uses the e-value to weight edges, instead",
-            "of the default Bit-Score."]
-        },
-        {
-          "opt": "--identity",
-          "description": ["If set, uses the identity to weight edges, instead",
-            "of the default Bit-Score."]
-        },
-        {
-          "opt": "--best-match",
-          "description": ["If set, it assumes best-matches instead reciprocal",
-            "best matches."]
-        },
-        {
-          "opt": "--mcl-bin",
-          "arg": "in_dir",
-          "description": ["Path to the directory containing the mcl binaries.",
-            "By default, assumed to be in the PATH."]
-        },
-        {
-          "name": "abc",
-          "arg": "out_file",
-          "opt": "--abc",
-          "description": "Use this abc file instead of a temporal file."
-        },
-        {
-          "opt": "--threads",
-          "arg": "integer",
-          "default": 2,
-          "description": "Number of threads to use."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "ogs.rb",
-      "description": ["Identifies Orthology Groups (OGs) in Reciprocal Best",
-        "Matches (RBM) between all pairs in a collection of genomes."],
-      "warn": ["This script suffers from chaining effect and is very",
-        "sensitive to spurious connections, because it applies a greedy",
-        "clustering algorithm. For most practical purposes, the use of this",
-        "script is discouraged and `ogs.mcl.rb` should be preferred."],
-      "help_arg": "--help",
-      "see_also": ["ogs.mcl.rb"],
-      "options": [
-        {
-          "opt": "--out",
-          "mandatory": true,
-          "arg": "out_file",
-          "description": "Output file containing the detected OGs."
-        },
-        {
-          "opt": "--dir",
-          "arg": "in_dir",
-          "description": "Directory containing the RBM files.",
-          "note": "Required unless --pre-ogs is passed."
-        },
-        {
-          "opt": "--pre-ogs",
-          "arg": "in_file",
-          "multiple_sep": ",",
-          "description": "Pre-computed OGs file(s), separated by commas."
-        },
-        {
-          "opt": "--unchecked",
-          "description": "Do not check internal redundancy in OGs."
-        },
-        {
-          "opt": "--format",
-          "arg": "string",
-          "default": "(\\S+)-(\\S+)\\.rbm",
-          "description": ["Format of the filenames for the RBM files (within",
-            "-d), using regex syntax."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "ogs.stats.rb",
-      "description": ["Estimates some descriptive statistics on a set of",
-        "Orthology Groups (OGs)."],
-      "see_also": ["ogs.mcl.rb"],
-      "help_arg": "--help",
-      "requires": [ { "ruby_gem": "json" } ],
-      "options": [
-        {
-          "opt": "--ogs",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input file containing the precomputed OGs."
-        },
-        {
-          "opt": "--json",
-          "arg": "out_file",
-          "description": "Output file in JSON format."
-        },
-        {
-          "opt": "--tab",
-          "arg": "out_file",
-          "description": "Output file in tabular format."
-        },
-        {
-          "opt": "--transposed-tab",
-          "arg": "out_file",
-          "description": "Output file in transposed tabular format."
-        },
-        {
-          "opt": "--auto",
-          "description": "Run completely quiertly (no STDERR or STDOUT)."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "clust.rand.rb",
-      "description": ["Calculates the Rand Index and the Adjusted Rand Index",
-        "between two clusterings. The clustering format is a raw text file",
-        "with one cluster per line, each defined as comma-delimited members,",
-        "and a header line (ignored). Note that this is equivalent to the OGs",
-        "format for 1 genome."],
-      "see_also": ["ogs.mcl.rb"],
-      "help_arg": "--help",
-      "cite": [
-        ["Rand, 1971, J Am Stat Assoc",
-          "https://doi.org/10.2307%2F2284239"],
-        ["Hubert & Arabie, 1985, J Classif",
-          "https://doi.org/10.1007%2FBF01908075"]
-      ],
-      "options": [
-        {
-          "name": "Input file 1",
-          "opt": "--clust1",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "First input file."
-        },
-        {
-          "name": "Input file 2",
-          "opt": "--clust2",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Second input file."
-        },
-        {
-          "name": "Precision",
-          "opt": "--prec",
-          "arg": "integer",
-          "description": "Precision to report.",
-          "default": 6
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    }
-  ]
-}