miga-base 0.7.25.2 → 0.7.25.3

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

@@ -1,355 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "BlastTab.kegg_pep2path_rest.pl",
-      "description": ["Takes a BLAST against KEGG_PEP (or KO) and retrieves",
-        "the pathways in which the subject peptides are involved."],
-      "requires": [
-        { "perl_lib": "JSON" },
-        { "perl_lib": "LWP::Simple" }
-      ],
-      "help_arg": "",
-      "options": [
-        {
-          "name": "blast.txt",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input tabular BLAST file."
-        },
-        {
-          "name": "Cache file",
-          "arg": "out_file",
-          "description": ["(optional) File containing the saved cache. If",
-            "unset, the cache won't be recoverable across instances of this",
-            "script. It is strongly recommended to set a file. Multiple",
-            "parallel instances of this script may use the same cache file."]
-        },
-        ">",
-        {
-          "name": "output.txt",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Tab-delimited output file, with the columns: (1)",
-            "Query ID, (2) Subject ID, (3) Pathway ID, (4) Pathway (reference)",
-            "description, (5) Organism."]
-        }
-      ]
-    },
-    {
-      "task": "M5nr.getSequences.rb",
-      "description": ["Downloads a set of sequences from M5nr with a given",
-        "functional annotation."],
-      "help_arg": "--help",
-      "requires": [
-        { "ruby_gem": "restclient" },
-        { "ruby_gem": "open-uri" },
-        { "ruby_gem": "JSON" }
-      ],
-      "options": [
-        {
-          "opt": "--function",
-          "arg": "string",
-          "mandatory": true,
-          "description": "Functional annotation."
-        },
-        {
-          "name": "Output file",
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "File containing the sequences."
-        },
-        {
-          "opt": "--max",
-          "arg": "integer",
-          "default": 0,
-          "description": ["Maximum number of sequences to download. Set to",
-            "0 to download all."]
-        },
-        {
-          "opt": "--recover",
-          "description": "If set, tries to recover a previous FastA."
-        },
-        {
-          "name": "URL",
-          "opt": "--url",
-          "arg": "string",
-          "default": "http://api.metagenomics.anl.gov/m5nr",
-          "description": "URL for M5nr API."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "EBIseq2tax.rb",
-      "description": ["Maps a list of EBI-supported IDs to their corresponding",
-        "NCBI taxonomy using EBI RESTful API."],
-      "warn": ["Avoid using this script on millions of entries at a time,",
-        "since each entry elicits requests to EBI and NCBI servers."],
-      "requires": [
-        { "ruby_gem": "nokogiri" }
-      ],
-      "see_also": ["NCBIacc2tax.rb"],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "IDs",
-          "opt": "--ids",
-          "arg": "string",
-          "description": "Comma-separated list of EBI IDs.",
-          "note": "Required unless 'Input file' is passed."
-        },
-        {
-          "name": "Input file",
-          "opt": "--infile",
-          "arg": "in_file",
-          "description": ["Raw text file containing the list of EBI IDs,",
-            "one per line."],
-          "note": "Required unless 'IDs' is passed."
-        },
-        {
-          "opt": "--database",
-          "arg": "string",
-          "default": "uniprotkb",
-          "description": "EBI database defining the EBI IDs."
-        },
-        {
-          "opt": "--ranks",
-          "arg": "string",
-          "description": "Comma-delimited list of taxonomic ranks to report.",
-          "default": "superkingdom,phylum,class,order,family,genus,species"
-        },
-        {
-          "opt": "--noheader",
-          "description": "Do not includ a header in the output."
-        },
-        {
-          "opt": "--taxids",
-          "description": "Return Taxonomy IDs instead of scientific names."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        }
-      ]
-    },
-    {
-      "task": "RefSeq.download.bash",
-      "description": ["Downloads a collection of sequences and/or annotations",
-        "from NCBI's RefSeq."],
-      "help_arg": "",
-      "requires": [
-        {
-          "description": "curl",
-          "test": "curl --version"
-        }
-      ],
-      "options": [
-        {
-          "name": "Organism",
-          "arg": "string",
-          "mandatory": true,
-          "description": ["The organism to download (e.g.,",
-            "Streptococcus_pneumoniae)."]
-        },
-        {
-          "name": "Extension",
-          "arg": "string",
-          "mandatory": true,
-          "default": ".*.gz",
-          "description": ["Extension to download. Common extensions include",
-            ".fna.gz (genomic sequences), .faa.gz (protein sequences),",
-            ".gff.gz (annotations), and .*.gz (all data)."]
-        },
-        {
-          "name": "Level",
-          "arg": "string",
-          "mandatory": true,
-          "default": "Any",
-          "description": ["Use only genomes with this assembly level. Common",
-            "levels are 'Complete Genome' and 'Contig'. By default, any",
-            "assembly level is allowed ('Any')."]
-        },
-        {
-          "name": "Directory",
-          "arg": "out_dir",
-          "description": ["Directory where the files are to be downladed.",
-            "By default, same as 'Organism'."]
-        }
-      ]
-    },
-    {
-      "task": "SRA.download.bash",
-      "description": ["Downloads the set of runs from a project, sample, or",
-        "experiment in SRA."],
-      "help_arg": "",
-      "requires": [
-        {
-          "description": "curl",
-          "test": "curl --version"
-        }
-      ],
-      "options": [
-        {
-          "name": "SRA ID",
-          "arg": "string",
-          "mandatory": true,
-          "description": "ID of the SRA Project, Sample, or Experiment."
-        },
-        {
-          "name": "dir",
-          "arg": "out_dir",
-          "description": ["Directory where the files are to be downladed. By",
-            "default, same as 'SRA ID'."]
-        }
-      ]
-    },
-    {
-      "task": "gi2tax.rb",
-      "description": ["Maps a list of NCBI GIs to their corresponding taxonomy",
-        "using the NCBI EUtilities."],
-      "warn": ["Avoid using this script on millions of entries at a time,",
-        "since each entry elicits two requests to NCBI's servers.",
-        "*IMPORTANT NOTE*: NCBI is phasing out support for GIs. Please use",
-        "acc.ver instead with NCBIacc2tax.rb."],
-      "requires": [
-        { "ruby_gem": "nokogiri" },
-        { "ruby_gem": "json" }
-      ],
-      "see_also": ["NCBIacc2tax.rb"],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "GIs",
-          "opt": "--gis",
-          "arg": "string",
-          "description": "Comma-separated list of GIs.",
-          "note": "Required unless 'Input file' is passed."
-        },
-        {
-          "name": "Input file",
-          "opt": "--infile",
-          "arg": "in_file",
-          "description": ["Raw text file containing the list of GIs, one per",
-            "line."],
-          "note": "Required unless 'GIs' is passed."
-        },
-        {
-          "opt": "--protein",
-          "description": ["Use if the GIs are proteins. Otherwise, GIs are",
-            "assumed to be from the Nuccore Database."]
-        },
-        {
-          "opt": "--ranks",
-          "arg": "string",
-          "description": "Taxonomic ranks to report, separated by commas.",
-          "default": "superkingdom,phylum,class,order,family,genus,species"
-        },
-        {
-          "name": "No header",
-          "opt": "--noheader",
-          "description": "Do not include a header in the output."
-        },
-        {
-          "name": "Tax IDs",
-          "opt": "--taxids",
-          "description": "Return Taxonomy IDs instead of scientific names."
-        },
-        {
-          "name": "Exact GI",
-          "opt": "--exact-gi",
-          "description": ["Returns only taxonomy associated with the exact GI",
-            "passed. By default, it attempts to update accession versions if",
-            "possible."]
-        },
-        {
-          "opt": "--ignore-missing",
-          "description": ["Does not report missing GIs in the output file. By",
-            "default, it reports GI and empty values for all other columns."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Tab-delimited table with GIs and taxonomic",
-            "classification."]
-        }
-      ]
-    },
-    {
-      "task": "NCBIacc2tax.rb",
-      "description": ["Maps a list of NCBI accessions to their corresponding",
-        "taxonomy using the NCBI EUtilities."],
-      "warn": ["Avoid using this script on millions of entries at a time,",
-        "since each entry elicits two requests to NCBI's servers."],
-      "requires": [
-        { "ruby_gem": "nokogiri" },
-        { "ruby_gem": "json" }
-      ],
-      "see_also": ["EBIseq2tax.rb"],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "Accessions",
-          "opt": "--acc",
-          "arg": "string",
-          "description": "Comma-separated list of accessions.",
-          "note": "Required unless 'Input file' is passed."
-        },
-        {
-          "name": "Input file",
-          "opt": "--infile",
-          "arg": "in_file",
-          "description": ["Raw text file containing the list of accessions,",
-            "one per line."],
-          "note": "Required unless 'Accessions' is passed."
-        },
-        {
-          "opt": "--protein",
-          "description": ["Use if the accessions are proteins. Otherwise,",
-            "accessions are assumed to be from the Nuccore Database."]
-        },
-        {
-          "opt": "--ranks",
-          "arg": "string",
-          "description": "Taxonomic ranks to report, separated by commas.",
-          "default": "superkingdom,phylum,class,order,family,genus,species"
-        },
-        {
-          "name": "No header",
-          "opt": "--noheader",
-          "description": "Do not include a header in the output."
-        },
-        {
-          "name": "Tax IDs",
-          "opt": "--taxids",
-          "description": "Return Taxonomy IDs instead of scientific names."
-        },
-        {
-          "opt": "--ignore-missing",
-          "description": ["Does not report missing accessions in the output",
-            "file. By default, it reports GI and empty values for all other",
-            "columns."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Tab-delimited table with accessions and taxonomic",
-            "classification."]
-        }
-      ]
-    }
-  ]
-}

data/utils/enveomics/Manifest/Tasks/sequence-identity.json

@@ -1,501 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "aai.rb",
-      "description": ["Calculates the Average Amino acid Identity between two",
-        "genomes."],
-      "help_arg": "--help",
-      "see_also": ["ani.rb", "rbm.rb"],
-      "cite": [
-        ["Konstantinidis & Tiedje, 2005, JBac",
-          "https://dx.doi.org/10.1128%2FJB.187.18.6258-6264.2005"],
-        ["Altschul et al, 2000, JMB (BLAST)",
-          "https://dx.doi.org/10.1016/S0022-2836(05)80360-2"],
-        ["Kent WJ, 2002, Genome Res (BLAT)",
-          "https://dx.doi.org/10.1101/gr.229202"],
-        ["Buchfink B, Xie C, Huson D, 2015, Nat Meth (Diamond)",
-          "https://dx.doi.org/10.1038/nmeth.3176"]
-      ],
-      "options": [
-        {
-          "name": "Sequence 1",
-          "opt": "--seq1",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "FastA file containing the genome 1 (proteins).",
-          "note": ["Alternatively, you can supply the NCBI-acc of a genome",
-            " (nucleotides) with the format ncbi:CP014272 instead of files."]
-        },
-        {
-          "name": "Sequence 2",
-          "opt": "--seq2",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "FastA file containing the genome 2.",
-          "note": ["Alternatively, you can supply the NCBI-acc of a genome",
-            " (nucleotides) with the format ncbi:NC_004337 instead of files."]
-        },
-        {
-          "name": "Length",
-          "opt": "--len",
-          "arg": "integer",
-          "description": "Minimum alignment length (in aa).",
-          "default": 0
-        },
-        {
-          "name": "Length fraction",
-          "opt": "--len-fraction",
-          "arg": "float",
-          "description": ["Minimum alignment length as a fraction of the",
-            "shorter sequence (range 0-1)."],
-          "default": 0.0
-        },
-        {
-          "name": "Identity",
-          "opt": "--id",
-          "arg": "float",
-          "description": "Minimum alignment identity (in %).",
-          "default": 20.0
-        },
-        {
-          "name": "Bit-score",
-          "opt": "--bitscore",
-          "arg": "float",
-          "description": "Minimum bit score (in bits).",
-          "default": 0.0
-        },
-        {
-          "opt": "--hits",
-          "arg": "float",
-          "description": "Minimum number of hits.",
-          "default": 50.0
-        },
-        {
-          "name": "Nucleotides",
-          "opt": "--nucl",
-          "description": ["The input sequences are nucleotides (genes), not",
-            "proteins."]
-        },
-        {
-          "name": "Max ACTG",
-          "opt": "--max-actg",
-          "arg": "float",
-          "default": 0.95,
-          "description": ["Maximum fraction of ACTGN in the sequences before",
-            "assuming nucleotides."]
-        },
-        {
-          "name": "Executables",
-          "opt": "--bin",
-          "arg": "in_dir",
-          "description": ["Path to the directory containing the binaries of",
-            "the search program."]
-        },
-        {
-          "opt": "--program",
-          "arg": "select",
-          "values": ["blast+","blast","blat","diamond"],
-          "default": "blast+",
-          "description": "Search program to be used.",
-          "note": ["Make sure that you have installed the search program you",
-            "want to use. If you have downloaded the program, but it's not",
-            "installed, please use the Executables option above."]
-        },
-        {
-          "opt": "--threads",
-          "arg": "integer",
-          "description": "Number of parallel threads to be used.",
-          "default": 1
-        },
-        {
-          "name": "SQLite3 DB",
-          "opt": "--sqlite3",
-          "arg": "out_file",
-          "description": ["Path to the SQLite3 database to create (or update)",
-            "with the results."]
-        },
-        {
-          "name": "Name 1",
-          "opt": "--name1",
-          "arg": "string",
-          "description": ["Name of Sequence 1 to use in SQLite3 DB. By default",
-            "determined by filename."]
-        },
-        {
-          "name": "Name 2",
-          "opt": "--name2",
-          "arg": "string",
-          "description": ["Name of Sequence 2 to use in SQLite3 DB. By default",
-            "determined by filename."]
-        },
-        {
-          "name": "Don't save RBM",
-          "opt": "--no-save-rbm",
-          "description": ["Don't save the reciprocal best matches in the",
-            "--sqlite3 database."]
-        },
-        {
-          "opt": "--lookup-first",
-          "description": ["Indicates if the AAI should be looked up first in",
-            "the database. Requires SQLite3 DB, Auto, Name 1, and Name 2.",
-            "Incompatible with Result, Tab, Out, and RBM."]
-        },
-        {
-          "name": "Precision",
-          "opt": "--dec",
-          "arg": "integer",
-          "default": 2,
-          "description": "Decimal positions to report."
-        },
-        {
-          "name": "RBM",
-          "opt": "--rbm",
-          "arg": "out_file",
-          "description": "Saves a file with the reciprocal best matches."
-        },
-        {
-          "opt": "--out",
-          "arg": "out_file",
-          "description": ["Saves a file describing the alignments used for",
-            "two-way AAI."]
-        },
-        {
-          "name": "Result",
-          "opt": "--res",
-          "arg": "out_file",
-          "description": "Saves a file with the final results."
-        },
-        {
-          "opt": "--tab",
-          "arg": "out_file",
-          "description": ["Saves a file with the final two-way results in a",
-            "tab-delimited form. The columns are (in that order): AAI,",
-            "standard deviation, proteins used, proteins in the smallest",
-            "genome."]
-        },
-        {
-          "opt": "--auto",
-          "description": ["ONLY outputs the AAI value in STDOUT (or nothing,",
-            "if calculation fails)."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "ani.rb",
-      "description": ["Calculates the Average Nucleotide Identity between two",
-        "genomes."],
-      "help_arg": "--help",
-      "see_also": ["aai.rb","rbm.rb","HMM.essential.rb"],
-      "cite": [
-        ["Konstantinidis & Tiedje, 2005, PNAS",
-          "http://dx.doi.org/10.1073%2Fpnas.0409727102"],
-        ["Altschul et al, 2000, JMB (BLAST)",
-          "http://dx.doi.org/10.1016/S0022-2836(05)80360-2"],
-        ["Kent WJ, 2002, Genome Res (BLAT)",
-          "https://dx.doi.org/10.1101/gr.229202"]
-      ],
-      "options": [
-        {
-          "name": "Sequence 1",
-          "opt": "--seq1",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "FastA file containing the genome 1.",
-          "note": ["Alternatively, you can supply an NCBI-acc with the format",
-            "ncbi:CP014272 instead of files."]
-        },
-        {
-          "name": "Sequence 2",
-          "opt": "--seq2",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "FastA file containing the genome 2.",
-          "note": ["Alternatively, you can supply an NCBI-acc with the format",
-            "ncbi:AE005174 instead of files."]
-        },
-        {
-          "name": "Window",
-          "opt": "--win",
-          "arg": "integer",
-          "description": "Window size in the ANI calculation (in bp).",
-          "default": 1000
-        },
-        {
-          "opt": "--step",
-          "arg": "integer",
-          "description": "Step size in the ANI calculation (in bp).",
-          "default": 200
-        },
-        {
-          "name": "Length",
-          "opt": "--len",
-          "arg": "integer",
-          "description": "Minimum alignment length (in bp).",
-          "default": 700
-        },
-        {
-          "name": "Identity",
-          "opt": "--id",
-          "arg": "float",
-          "description": "Minimum alignment identity (in %).",
-          "default": 70.0
-        },
-        {
-          "opt": "--hits",
-          "arg": "integer",
-          "description": "Minimum number of hits.",
-          "default": 50
-        },
-        {
-          "name": "No correction",
-          "opt": "--nocorrection",
-          "description": "Report values without post-hoc correction."
-        },
-        {
-          "name": "Min ACTG",
-          "opt": "--min-actg",
-          "arg": "float",
-          "default": 0.95,
-          "description": ["Minimum fraction of ACTGN in the sequences before",
-            "assuming proteins."]
-        },
-        {
-          "name": "Executables",
-          "opt": "--bin",
-          "arg": "in_dir",
-          "description": ["Directory containing the binaries of the search",
-            "program."]
-        },
-        {
-          "opt": "--program",
-          "arg": "select",
-          "values": ["blast+", "blast", "blat"],
-          "default": "blast+",
-          "description": "Search program to be used.",
-          "note": ["Make sure that you have installed the search program you",
-            "want to use. If you have downloaded the program, but it's not",
-            "installed, please use the Executables option above."]
-        },
-        {
-          "opt": "--threads",
-          "arg": "integer",
-          "description": "Number of parallel threads to be used.",
-          "default": 1
-        },
-        {
-          "name": "SQLite3 DB",
-          "opt": "--sqlite3",
-          "arg": "out_file",
-          "description": ["Path to the SQLite3 database to create (or update)",
-            "with the results."]
-        },
-        {
-          "name": "Name 1",
-          "opt": "--name1",
-          "arg": "string",
-          "description": ["Name of Sequence 1 to use in SQLite3 DB. By default",
-            "it's determined by the filename."]
-        },
-        {
-          "name": "Name 2",
-          "opt": "--name2",
-          "arg": "string",
-          "description": ["Name of Sequence 2 to use in SQLite3 DB. By default",
-            "it's determined by the filename."]
-        },
-        {
-          "name": "Don't save regions",
-          "opt": "--no-save-regions",
-          "description": "Don't save the fragments in the SQLite3 database."
-        },
-        {
-          "name": "Don't save RBM",
-          "opt": "--no-save-rbm",
-          "description": ["Don't save the reciprocal best matches in the",
-            "--sqlite3 database."]
-        },
-        {
-          "opt": "--lookup-first",
-          "description": ["Indicates if the ANI should be looked up first in",
-            "the database. Requires SQLite3 DB, Auto, Name 1, and Name 2.",
-            "Incompatible with Result, Tab, and Out."]
-        },
-        {
-          "name": "Precision",
-          "opt": "--dec",
-          "arg": "integer",
-          "description": "Decimal positions to report.",
-          "default": 2
-        },
-        {
-          "opt": "--out",
-          "arg": "out_file",
-          "description": ["Saves a file describing the alignments used for",
-            "two-way ANI."]
-        },
-        {
-          "name": "Result",
-          "opt": "--res",
-          "arg": "out_file",
-          "description": "Saves a file with the final results."
-        },
-        {
-          "opt": "--tab",
-          "arg": "out_file",
-          "description": ["Saves a file with the final two-way results in a",
-            "tab-delimited form. The columns are (in that order): ANI,",
-            "standard deviation, fragments used, fragments in the smallest",
-            "genome."]
-        },
-        {
-          "opt": "--auto",
-          "description": ["ONLY outputs the ANI value in STDOUT (or nothing,",
-            "if calculation fails)."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "HMM.haai.rb",
-      "description": ["Estimates Average Amino Acid Identity (AAI) from the",
-        "essential genes extracted and aligned by HMM.essential.rb (see",
-        "Alignments)."],
-      "help_arg": "--help",
-      "see_also": ["HMM.essential.rb","aai.rb"],
-      "options": [
-        {
-          "name": "Alignments 1",
-          "opt": "-1",
-          "arg": "in_file",
-          "description": "Input alignments file for genome 1."
-        },
-        {
-          "name": "Alignments 2",
-          "opt": "-2",
-          "arg": "in_file",
-          "description": "Input alignments file for genome 2."
-        },
-        {
-          "name": "Alignment output",
-          "opt": "--aln-out",
-          "arg": "out_file",
-          "description": "Output file containing the aligned proteins."
-        },
-	{
-	  "opt": "--components",
-	  "arg": "out_file",
-	  "description": ["Output file containing the components of the",
-	    "estimation. Tab-delimited file with model name, matches, and",
-	    "columns."]
-	},
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "rbm.rb",
-      "description": ["Finds the reciprocal best matches between two sets of",
-        "sequences."],
-      "help_arg": "--help",
-      "cite":[
-        ["Altschul et al, 2000, JMB (BLAST)",
-          "http://dx.doi.org/10.1016/S0022-2836(05)80360-2"],
-        ["Buchfink B, Xie C, Huson D, 2015, Nat Meth (Diamond)",
-          "https://dx.doi.org/10.1038/nmeth.3176"]
-      ],
-      "options": [
-        {
-          "name": "Sequence 1",
-          "opt": "--seq1",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "FastA file containing the genome 1."
-        },
-        {
-          "name": "Sequence 2",
-          "opt": "--seq2",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "FastA file containing the genome 2."
-        },
-        {
-          "name": "Nucleotides",
-          "opt": "--nucl",
-          "description": ["Sequences are assumed to be nucleotides (proteins",
-            "by default)."]
-        },
-        {
-          "name": "Length",
-          "opt": "--len",
-          "arg": "integer",
-          "description": "Minimum alignment length (in residues).",
-          "default": 0
-        },
-        {
-          "name": "Fraction",
-          "opt": "--fract",
-          "arg": "float",
-          "default": 0.0,
-          "description": ["Minimum alignment length (as a fraction of the",
-            "query). If set, requires BLAST+ or Diamond (see Program)."]
-        },
-        {
-          "name": "Identity",
-          "opt": "--id",
-          "arg": "float",
-          "description": "Minimum alignment identity (in %).",
-          "default": 0.0
-        },
-        {
-          "name": "Bit score",
-          "opt": "--score",
-          "arg": "float",
-          "default": 0.0,
-          "description": "Minimum alignment score (in bits)."
-        },
-        {
-          "name": "Executables",
-          "opt": "--bin",
-          "arg": "in_dir",
-          "description": ["Directory containing the binaries of the search",
-            "program."]
-        },
-        {
-          "opt": "--program",
-          "arg": "select",
-          "values": ["blast+", "blast", "blat", "diamond"],
-          "default": "blast+",
-          "description": "Search program to be used. Default: blast+.",
-          "note": ["Make sure that you have installed the search program you",
-            "want to use. If you have downloaded the program, but it's not",
-            "installed, please use the Executables option above."]
-        },
-        {
-          "opt": "--threads",
-          "arg": "integer",
-          "description": "Number of parallel threads to be used.",
-          "default": 1
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Reciprocal Best Matches in BLAST tabular format."
-        }
-      ]
-    }
-  ]
-}