miga-base 1.2.15.1 → 1.2.15.3

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

@@ -1,906 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "Aln.cat.rb",
-      "description": ["Concatenates several multiple alignments in FastA",
-        "format into a single multiple alignment. The IDs of the sequences",
-        "(or the ID prefixes, if using --ignore-after) must coincide across",
-        "files."],
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--coords",
-          "arg": "out_file",
-          "description": "Output file of coordinates in RAxML-compliant format."
-        },
-        {
-          "opt": "--ignore-after",
-          "arg": "string",
-          "description": ["Remove everything in the IDs after the specified",
-            "string."]
-        },
-        {
-          "opt": "--remove-invariable",
-          "description": "Remove invariable sites.",
-          "note": ["Invariable sites are defined as columns with only one",
-            "state and undefined characters. Additional ambiguous characters",
-            "may exist and should be declared using --undefined."]
-        },
-        {
-          "opt": "--missing-char",
-          "description": "Character denoting missing data.",
-          "arg": "character",
-          "default": "-"
-        },
-        {
-          "opt": "--model",
-          "description": "Name of the model to use if --coords is used.",
-          "note": "See RAxML's documentation for additional information.",
-          "arg": "string",
-          "default": "AUTO"
-        },
-        {
-          "opt": "--undefined",
-          "arg": "string",
-          "description": ["All characters to be regarded as 'undefined'. It",
-            "should include all ambiguous and missing data chars. Ignored",
-            "unless --remove-invariable."],
-          "default": "-.Xx?"
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        },
-        {
-          "name": "Input alignments",
-          "arg": "in_file",
-          "multiple_sep": " ",
-          "mandatory": true,
-          "description": "Input alignments in FastA format."
-        },
-        ">",
-        {
-          "name": "Output alignment",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output concatenated alignment."
-        }
-      ]
-    },
-    {
-      "task": "Aln.convert.pl",
-      "description": "Translates between different alignment formats.",
-      "help_arg": "",
-      "requires": [
-        {
-          "perl_lib": "Bio::AlignIO"
-        }
-      ],
-      "cite": [["Stajich et al, 2002, GRes",
-        "http://dx.doi.org/10.1101/gr.361602"]],
-      "options": [
-        {
-          "name": "In-format",
-          "description": "Input file's format.",
-          "mandatory": true,
-          "arg": "select",
-          "values": ["bl2seq", "clustalw", "emboss", "fasta", "maf", "mase",
-            "mega", "meme", "metafasta", "msf", "nexus", "pfam", "phylip", "po",
-            "prodom", "psi", "selex", "stockholm", "XMFA", "arp"]
-        },
-        {
-          "name": "Out-format",
-          "description": "Output file's format.",
-          "mandatory": true,
-          "arg": "select",
-          "values": ["bl2seq", "clustalw", "emboss", "fasta", "maf", "mase",
-            "mega", "meme", "metafasta", "msf", "nexus", "pfam", "phylip", "po",
-            "prodom", "psi", "selex", "stockholm", "XMFA", "arp"]
-        },
-        "<",
-        {
-          "arg": "in_file",
-          "mandatory": true
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true
-        }
-      ]
-    },
-    {
-      "task": "AlphaDiversity.pl",
-      "description": ["Takes a table of OTU abundance in one or more samples",
-        "and calculates the Rao (Q_alpha), Rao-Jost (Q_alpha_eqv), Shannon",
-        "(Hprime), and inverse Simpson (1_lambda) indices of alpha diversity",
-        "for each sample."],
-      "help_arg": "--help",
-      "see_also": ["Chao1.pl"],
-      "options": [
-        {
-          "name": "Input table",
-          "opt": "-i",
-          "arg": "in_file",
-          "description": ["Columns: samples, rows: OTUs, first column: OTU",
-            "names)."],
-          "mandatory": true
-        },
-        {
-          "name": "Discard rows",
-          "opt": "-r",
-          "arg": "integer",
-          "description": "Number of rows to ignore.",
-          "default": 0
-        },
-        {
-          "name": "Discard left columns",
-          "opt": "-c",
-          "arg": "integer",
-          "description": ["Number of columns to ignore after the first column",
-            "(i.e., between the first column, containing the name of the",
-            "categories, and the first column of abundance values)."],
-          "default": 0
-        },
-        {
-          "name": "Discard right columns",
-          "opt": "-C",
-          "arg": "integer",
-          "description": "Number of columns to ignore at the end of each line.",
-          "default": 0
-        },
-        {
-          "name": "Delimiter",
-          "opt": "-d",
-          "arg": "string",
-          "description": "Character (or string) separating columns.",
-          "note": ["Supported escaped characters are: '\\t' (tabulation), and",
-            "'\\0' (null bit)."],
-          "default": "\\t"
-        },
-        {
-          "name": "Headers",
-          "opt": "-h",
-          "description": ["The first row is assumed to have the names of the",
-            "samples."]
-        },
-        {
-          "name": "Distances file",
-          "opt": "-D",
-          "arg": "in_file",
-          "description": ["A squared matrix (or bottom-left half matrix) with",
-            "the distances between categories (OTUs or functions). The first",
-            "column must contain the names of the categories, and it shouldn't",
-            "have headers. If not set, all distances are assumed to be one."],
-          "note": "Only used for Rao."
-        },
-        {
-          "name": "Skip Rao",
-          "opt": "-R",
-          "description": "Do not calculate Rao indices.",
-          "note": ["This significantly decreases the total running time. Note",
-            "that Rao indices are highly susceptible to precision errors, and",
-            "shouldn't be trusted for very big numbers."]
-        },
-        {
-          "name": "q for qD",
-          "opt": "-q",
-          "arg": "integer",
-          "description": "Estimate the qD index (true diversity order q).",
-          "default": 0
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true
-        }
-      ]
-    },
-    {
-      "task": "Chao1.pl",
-      "description": ["Takes a table of OTU abundance in one or more samples",
-        "and calculates the chao1 index (with 95% Confidence Interval) for",
-        "each sample. To use it with Qiime OTU Tables, run it ignoring 1",
-        "left column and with header."],
-      "cite": [["Chao, 1984, Scandinavian J Stat",
-        "http://www.jstor.org/stable/4615964"]],
-      "see_also": ["AlphaDiversity.pl"],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "Input file",
-          "opt": "-i",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input table (columns:samples, rows:OTUs)."
-        },
-        {
-          "name": "Rows",
-          "opt": "-r",
-          "arg": "integer",
-          "default": 0,
-          "description": "Number of rows to ignore."
-        },
-        {
-          "name": "Left columns to ignore",
-          "opt": "-c",
-          "arg": "integer",
-          "default": 0,
-          "description": "Number of columns to ignore."
-        },
-        {
-          "name": "Right columns to ignore",
-          "opt": "-C",
-          "arg": "integer",
-          "default": 0,
-          "description": "Number of columns to ignore at the end."
-        },
-        {
-          "name": "Delimiter",
-          "opt": "-d",
-          "arg": "string",
-          "default": "\\t",
-          "description": "Delimiter between columns.",
-          "note": ["Supported escaped characters are: \\t (tabulation),",
-            "and \\0 (null bit)."]
-        },
-        {
-          "name": "Header",
-          "opt": "-h",
-          "description": ["If set, the first row is assumed to have the names",
-            "of the samples."]
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Chao1 index and 95% CI bounds for each sample, in",
-            "tab-delimited format."]
-        }
-      ]
-    },
-    {
-      "task": "CharTable.classify.rb",
-      "description": ["Uses a dichotomous key to classify objects parsing a",
-        "character table."],
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--table",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Input table containing the states (columns) per",
-            "object (row). It must be tab-delimited and with row and column",
-            "names."]
-        },
-        {
-          "opt": "--key",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Input table containing the dychotomous key in",
-            "linked style, defined in four columns (can contain #-lead comment",
-            "lines): (1) ID of the step, typically a sequential integer. (2)",
-            "Name of character to evaluate. Must coincide with the -t headers.",
-            "(3) First character decision (see below). (4) Second character",
-            "decision (see below).\nA character decision must be formated as:",
-            "state (must coincide with the values in -t), colon (:), step to",
-            "follow. If the state is * (star) any state triggers the decision",
-            "(this should be the norm in column 4). The step to follow should",
-            "be a step ID in square brackets, or the name of the",
-            "classification."]
-        },
-        {
-          "opt": "--classification",
-          "arg": "out_file",
-          "description": ["Two-column table with the classification of the",
-            "input objects."]
-        },
-        {
-          "opt": "--newick",
-          "arg": "out_file",
-          "description": ["Tree containing all the classified objects. This",
-            "only makes sense for synoptic keys."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "GenBank.add_fields.rb",
-      "description": "Adds annotations to GenBank files.",
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--genbank",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input GenBank file."
-        },
-        {
-          "opt": "--table",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Input file containing the annotations. It must be a",
-            "tab-delimited raw table including a header row with the names of",
-            "the fields."]
-        },
-        {
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output file containing the annotated GenBank."
-        },
-        {
-          "opt": "--key",
-          "arg": "integer",
-          "default": 1,
-          "description": "Key of the column to use as identifier."
-        },
-        {
-          "opt": "--split",
-          "arg": "string",
-          "default": "#",
-          "description": ["String that separates multiple entries in the",
-            "annotation features."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "HMM.essential.rb",
-      "description": ["Finds and extracts a collection of essential proteins",
-        "suitable for genome completeness evaluation and phylogenetic",
-        "analyses in Archaea and Bacteria."],
-      "warn": ["Most complete bacterial genomes contain only 106/111 genes in",
-        "this collection, therefore producing a completeness of 95.5%, and",
-        "most archaeal genomes only contain 26/111 genes, producing a",
-        "completeness of 23.4%. Use the options --bacteria and/or --archaea to",
-        "ignore models often missing in one or both domains. Note that even",
-        "with these options, some complete archaeal genomes result in very low",
-        "values of completeness (e.g., Nanoarchaeum equitans returns 88.5%)."],
-      "help_arg": "--help",
-      "requires": [
-        {
-          "description": "HMMer 3.0+",
-          "test": "hmmsearch -h",
-          "source_url": "http://hmmer.janelia.org/software"
-        }
-      ],
-      "cite": [
-        ["Eddy, 2011, PLoS CB",
-          "http://dx.doi.org/10.1371/journal.pcbi.1002195"],
-        ["Dupont et al, 2012, ISME J",
-          "https://doi.org/10.1038/ismej.2011.189"],
-        ["Rodriguez-R et al, 2014, ISME J",
-          "https://doi.org/10.1038/ismej.2015.5"],
-        ["Lee, 2019, Bioinf",
-          "https://doi.org/10.1093/bioinformatics/btz188"],
-        ["Eren et al, 2015, PeerJ",
-          "https://doi.org/10.7717/peerj.1319"]
-      ],
-      "options": [
-        {
-          "name": "Input file",
-          "opt": "--in",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "FastA file containing all the proteins in the genome."
-        },
-        {
-          "opt": "--collection",
-          "arg": "string",
-          "default": "dupont_2012",
-          "description": ["Reference collection of essential proteins to use.",
-            "One of: dupont_2012 (default, Dupont et al 2012 modified by",
-            "Rodriguez-R et al 2015), or lee_2019 (Lee 2019 modified by Eren",
-            "et al 2015)."]
-        },
-        {
-          "name": "Output file",
-          "opt": "--out",
-          "arg": "out_file",
-          "description": ["FastA file with the translated essential genes. By",
-            "default the file is not produced."]
-        },
-        {
-          "opt": "--per-model",
-          "arg": "out_file",
-          "description": ["Prefix of translated genes in independent files",
-            "with the name of the model appended. By default files are not",
-            "produced."]
-        },
-        {
-          "opt": "--report",
-          "arg": "out_file",
-          "description": ["Path to the report file. By default, the report is",
-            "sent to the STDOUT."]
-        },
-        {
-          "name": "HMMsearch output",
-          "opt": "--hmm-out",
-          "arg": "out_file",
-          "description": ["Save HMMsearch output in this file. By default,",
-            "not saved."]
-        },
-        {
-          "opt": "--alignments",
-          "opt": "out_file",
-          "description": ["Save the aligned proteins in this file. By default,",
-            "not saved."]
-        },
-        {
-          "opt": "--bacteria",
-          "description": "If set, ignores models typically missing in Bacteria."
-        },
-        {
-          "opt": "--archaea",
-          "description": "If set, ignores models typically missing in Archaea."
-        },
-        {
-          "opt": "--genome-eq",
-          "description": ["If set, ignores models not suitable for",
-            "genome-equivalents estimations. See Rodriguez-R et al, 2015, ISME",
-            "J 9(9):1928-1940."],
-          "source_url": "http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej20155a.html"
-        },
-        {
-          "opt": "--rename",
-          "arg": "string",
-          "description": ["If set, renames the sequences with the string",
-            "provided and appends it with pipe (|) and the gene name (except",
-            "in --per-model files)."]
-        },
-        {
-          "opt": "--no-stats",
-          "description": ["If set, no statistics are reported on genome",
-            "evaluation."]
-        },
-        {
-          "opt": "--no-genes",
-          "description": ["If set, statistics won't include the lists of",
-            "missing/multi-copy genes."]
-        },
-        {
-          "opt": "--metagenome",
-          "description": ["If set, it allows for multiple copies of each gene",
-            "and turns on metagenomic report mode."]
-        },
-        {
-          "opt": "--list-models",
-          "description": ["If set, it only lists the models and exits.",
-            "Compatible with 'Archaea', 'Bacteria', 'Genome eq', and 'Quiet';",
-            "ignores all other parameters."]
-        },
-        {
-          "opt": "--bin",
-          "arg": "in_dir",
-          "description": "Directory containing the binaries of HMMer 3.0+."
-        },
-        {
-          "opt": "--model-file",
-          "arg": "in_file",
-          "description": "External file containing models to search."
-        },
-        {
-          "opt": "--threads",
-          "arg": "integer",
-          "default": 2,
-          "description": "Number of parallel threads to be used."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "HMMsearch.extractIds.rb",
-      "description": ["Extracts the sequence IDs and query model form a",
-        "(multiple) HMMsearch report (for HMMer 3.0)."],
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--all-evalue",
-          "arg": "float",
-          "description": "Maximum e-value of sequence to report result."
-        },
-        {
-          "opt": "--all-score",
-          "arg": "float",
-          "description": "Minimum score of sequence to report result."
-        },
-        {
-          "opt": "--best-evalue",
-          "arg": "float",
-          "description": "Maximum e-value of best domain to report result."
-        },
-        {
-          "opt": "--best-score",
-          "arg": "float",
-          "description": "Minimum score of best domain to report result."
-        },
-        {
-          "opt": "--no-model",
-          "description": "Do not include the query model in the output list."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        },
-        "<",
-        {
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input HMMsearch text file."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output list of IDs."
-        }
-      ]
-    },
-    {
-      "task": "JPlace.distances.rb",
-      "description": ["Extracts the distance (estimated branch length) of each",
-        "placed read to a given node in a JPlace file."],
-      "requires": [ { "ruby_gem": "json" } ],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "Input file",
-          "opt": "--in",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ".jplace input file containing the read placement."
-        },
-        {
-          "name": "Node",
-          "opt": "--node",
-          "arg": "string",
-          "mandatory": true,
-          "description": ["Index (number in curly brackets) of the node to",
-            "which distances should be measured."]
-        },
-        {
-          "name": "Output file",
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output file in tabular format."
-        },
-        {
-          "opt": "--in-node",
-          "arg": "string",
-          "description": ["Report only reads placed at this node or it's",
-            "children."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "JPlace.to_iToL.rb",
-      "description": ["Generates iToL-compatible files from a .jplace file",
-        "(produced by RAxML's EPA or pplacer), that can be used to draw",
-        "pie-charts in the nodes of the reference tree."],
-      "requires": [ { "ruby_gem": "json" } ],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "Input file",
-          "opt": "--in",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ".jplace input file containing the read placement."
-        },
-        {
-          "name": "Out base",
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Base of the output files."
-        },
-        {
-          "opt": "--unique",
-          "arg": "string",
-          "description": ["Name of the dataset (if only one is used).",
-            "Conflicts with 'Regex' and 'Separator'."]
-        },
-        {
-          "opt": "--regex",
-          "arg": "string",
-          "description": ["Regular expression capturing the sample ID (named",
-            "dataset) in read names. By default: '^(?<dataset>.+?):.*'.",
-            "Conflicts with 'Separator'."]
-        },
-        {
-          "opt": "--separator",
-          "arg": "string",
-          "description": ["String separating the dataset name and the rest of",
-            "the read name. It assumes that the read name starts by the",
-            "dataset name. Conflicts with 'Regex'."]
-        },
-        {
-          "opt": "--metadata",
-          "arg": "in_file",
-          "description": ["Datasets metadata in tab-delimited format with a",
-            "header row. Valid headers: name (required), color (in Hex),",
-            "size (# reads), norm (any float)."]
-        },
-        {
-          "opt": "--norm",
-          "arg": "string",
-          "description": ["Normalization strategy. Must be one of:\n",
-            "none: Direct read counts are reported without normalization.\n",
-            "count (default): The counts are normalized (divided) by the total",
-            "counts per dataset.\n",
-            "size: The counts are normalized (divided) by the size column in",
-            "metadata (must be integer).\n",
-            "norm: The counts are normalized (divided) by the norm column in",
-            "metadata (can be any float)."]
-        },
-        {
-          "opt": "--old-itol",
-          "description": ["Generate output file using the old iToL format",
-            " (pre v3.0)."]
-        },
-        {
-          "opt": "--collapse",
-          "arg": "in_file",
-          "description": "Internal nodes to collapse (requires rootted tree)."
-        },
-        {
-          "opt": "--area",
-          "description": ["If set, the area of the pies is proportional to the",
-            "placements. Otherwise, the radius is."]
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "MyTaxa.fragsByTax.pl",
-      "description": "Identifies fragments annotated as a taxon in MyTaxa.",
-      "help_arg": "",
-      "options": [
-        {
-          "name": "MyTaxa output",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Classification file generated by MyTaxa."
-        },
-        {
-          "name": "Taxon",
-          "arg": "string",
-          "mandatory": true,
-          "description": "Taxon to look for."
-        },
-        {
-          "name": "Rank",
-          "arg": "string",
-          "description": "Rank of taxon (optional). By default: any rank."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "List of fragment IDs."
-        }
-      ]
-    },
-    {
-      "task": "MyTaxa.seq-taxrank.rb",
-      "description": ["Generates a simple tabular file with the classification",
-        "of each sequence at a given taxonomic rank from a MyTaxa output."],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "MyTaxa",
-          "opt": "--mytaxa",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input MyTaxa file."
-        },
-        {
-          "opt": "--rank",
-          "arg": "string",
-          "default": "genus",
-          "description": "Taxonomic rank."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        }
-      ]
-    },
-    {
-      "task": "Taxonomy.silva2ncbi.rb",
-      "description": ["Re-formats Silva taxonomy into NCBI-like taxonomy dump",
-        "files."],
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--silvaranks",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Input Silva ranks file (e.g.,",
-            "tax_ranks_ssu_115.txt)."],
-          "source_url": "https://www.arb-silva.de/no_cache/download/archive/release_115/Exports/"
-        },
-        {
-          "opt": "--silvaref",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Input Silva ref alignment file (e.g.,",
-            "SSURef_NR99_115_tax_silva_full_align_trunc.fasta)."],
-          "source_url": "https://www.arb-silva.de/no_cache/download/archive/release_115/Exports/"
-        },
-        {
-          "opt": "--patch",
-          "arg": "in_file",
-          "description": ["If passed, it replaces the paths specified in the",
-            "patch."],
-          "source_url": "http://enve-omics.ce.gatech.edu/data/public_misc/patch_Silva_SSU_r115.txt"
-        },
-        {
-          "opt": "--seqinfo",
-          "arg": "out_file",
-          "description": ["If passed, it creates a CSV seq-info file",
-            "compatible with taxtastic."]
-        },
-        {
-          "opt": "--taxfile",
-          "arg": "out_file",
-          "description": "If passed, it creates a simple TSV taxonomy file."
-        },
-        {
-          "opt": "--ncbi",
-          "arg": "out_dir",
-          "description": ["If passed, output folder for the NCBI dump files",
-            "(e.g., taxdmp)."]
-        },
-        {
-          "opt": "--warns",
-          "description": "Verbously display warnings."
-        }
-      ]
-    },
-    {
-      "task": "GFF.catsbj.pl",
-      "description": ["Generates a list of coordinates from a GFF table",
-        "concatenating the subject sequences."],
-      "help_arg": "-h",
-      "see_also": ["BlastTab.recplot2.R", "BlastTab.catsbj.pl"],
-      "options": [
-        {
-          "name": "Lim file",
-          "opt": "-L",
-          "arg": "out_file",
-          "description": ["An output file with the absolute coordinates of the",
-            "concatenated contigs. This is identical to the .lim file",
-            "generated by BlastTab.catsbj.pl."]
-        },
-        {
-          "name": "Inter-feature gaps",
-          "opt": "-i",
-          "description": ["Preserve exact coordinates and include",
-            "inter-feature windows as separate bins. By default, the",
-            "coordinates are set in the midpoint between features when",
-            "non-contiguous."]
-        },
-        {
-          "name": "Subset",
-          "opt": "-s",
-          "description": ["The FastA provided is to be treated as a subset of",
-            "the subject. By default, it expects all the contigs to be present",
-            "in the BLAST."]
-        },
-        {
-          "name": "Quiet",
-          "opt": "-q",
-          "description": "Run quietly."
-        },
-        {
-          "name": "Subject sequences",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Subject sequences (contigs) in FastA format."
-        },
-        {
-          "name": "Features",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Features to map in GFF."
-        }
-      ]
-    },
-    {
-      "task": "Table.prefScore.R",
-      "description": ["Estimate preference score of species based on occupancy",
-        "in biased sample sets."],
-      "help_arg": "--help",
-      "requires": [ { "r_package": "optparse" } ],
-      "options": [
-        {
-          "name": "Occupancy matrix",
-          "opt": "--x",
-          "arg": "in_file",
-          "description": ["A tab-delimited table of presence/absence (1/0)",
-            "with species as rows and samples as columns."],
-          "mandatory": true
-        },
-        {
-          "name": "Sample set",
-          "opt": "--set",
-          "arg": "in_file",
-          "description": ["A list of sample names that constitute the test",
-            "set, one per line."],
-          "mandatory": true
-        },
-        {
-          "opt": "--ignore",
-          "arg": "in_file",
-          "description": ["A list of species to exclude from the analysis,",
-            "one per line."]
-        },
-        {
-          "name": "Significance threshold",
-          "opt": "--signif-thr",
-          "arg": "float",
-          "description": "Absolute value of the significance threshold."
-        },
-        {
-          "opt": "--col-above",
-          "arg": "string",
-          "description": "Color for points significantly above zero.",
-          "default": "#941100"
-        },
-        {
-          "opt": "--col-equal",
-          "arg": "string",
-          "description": ["Color for points not significantly different from",
-            "zero."],
-          "default": "#BDBDBD"
-        },
-        {
-          "opt": "--col-below",
-          "arg": "string",
-          "description": "Color for points significantly below zero.",
-          "default": "#2F5496"
-        },
-        {
-          "name": "Output preference scores",
-          "arg": "out_file",
-          "description": "Output raw-text file with preference scores.",
-          "mandatory": true
-        },
-        {
-          "name": "Graphical utput",
-          "arg": "out_file",
-          "description": "Output PDF file with preference scores plot."
-        },
-        {
-          "name": "Width",
-          "arg": "float",
-          "description": "Width of the plot in inches (7 by default)."
-        },
-        {
-          "name": "Height",
-          "arg": "float",
-          "description": "Height of the plot in inches (7 by default)."
-        }
-      ]
-    }
-  ]
-}