miga-base 1.2.15.2 → 1.2.15.4

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

@@ -1,790 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "BlastTab.addlen.rb",
-      "description": ["Appends an extra column to a tabular BLAST with the",
-        "length of the query or the subject sequence."],
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--fasta",
-          "arg": "in_file",
-          "description": "FastA file of the query or the subject.",
-          "mandatory": true
-        },
-        {
-          "opt": "--subject",
-          "description": ["Use the subject column of the BLAST, by default the",
-            "query column is used."],
-          "note": "If used, the input FastA must contain subject sequences."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        },
-        "<",
-        {
-          "arg": "in_file",
-          "description": "Input tabular BLAST file.",
-          "mandatory": true
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "description": "Output tabular BLAST file with additional column.",
-          "mandatory": true
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.advance.bash",
-      "description": ["Calculates the percentage of a partial BLAST result.",
-        "The value produced slightly subestimates the actual advance, due to",
-        "un-flushed output and trailing queries that could be processed but",
-        "generate no results."],
-      "help_arg": "",
-      "requires": [ { "interpreter": "awk" } ],
-      "options": [
-        {
-          "name": "Blast",
-          "arg": "in_file",
-          "description": "Incomplete Tabular BLAST output.",
-          "mandatory": true
-        },
-        {
-          "name": "Query FastA",
-          "arg": "in_file",
-          "description": "FastA file with query sequences.",
-          "mandatory": true
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.best_hit_sorted.pl",
-      "description": "Filters a tabular BLAST to retain only the best matches.",
-      "help_arg": "--help",
-      "see_also": ["BlastTab.topHits_sorted.rb"],
-      "options": [
-        {
-          "name": "Sort",
-          "arg": "select",
-          "values": ["sort","cat"],
-          "mandatory": true,
-          "description": ["Use 'sort' if your BLAST is not pre-sorted by the",
-            "first column (or if you're not sure). Use 'cat' otherwise."]
-        },
-        {
-          "name": "Input BLAST",
-          "arg": "in_file",
-          "multiple_sep": " ",
-          "mandatory": true,
-          "description": "Tabular BLAST file to filter."
-        },
-        "|",
-        { "arg": "task" },
-        ">",
-        {
-          "name": "Output BLAST",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Filetered tabular BLAST output."
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.catsbj.pl",
-      "description": ["Generates a list of hits from a BLAST result",
-        "concatenating the subject sequences. This can be used, e.g., to",
-        "analyze BLAST results against draft genomes. This script creates two",
-        "files using <map.bls> as prefix with extensions .rec (for the",
-        "recruitment plot) and .lim (for the limits of the different sequences",
-        "in <seq.fa>)."],
-      "see_also": ["BlastTab.recplot2.R", "GFF.catsbj.pl"],
-      "help_arg": "-h",
-      "options": [
-         {
-           "opt": "-i",
-           "name": "Identity",
-           "description": "Minimum identity (in %) to report a result.",
-           "arg": "float",
-           "default": 70.0
-         },
-         {
-           "opt": "-l",
-           "name": "Length",
-           "description": "Minimum alignment length to report a result.",
-           "default": 60.0,
-           "arg": "float"
-         },
-         {
-           "opt": "-s",
-           "name": "Subset",
-           "description": ["The FastA provided is to be treated as a subset of",
-             "the subject. By default, it expects all the BLAST subjects to be",
-             "present in the FastA."]
-         },
-         {
-           "opt": "-q",
-           "name": "Quiet",
-           "description": "Run quietly."
-         },
-         {
-           "name": "seq.fa",
-           "description": "Subject sequences (ref) in FastA format.",
-           "mandatory": true,
-           "arg": "in_file"
-         },
-         {
-           "name": "map.bls",
-           "description": ["Mapping of the reads to the reference in Tabular",
-             "BLAST format."],
-           "mandatory": true,
-           "arg": "in_file"
-         }
-      ]
-    },
-    {
-      "task": "BlastTab.cogCat.rb",
-      "description": ["Replaces the COG gene IDs in a BLAST for the COG",
-        "category."],
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--whog",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "COG's 'whog' file."
-        },
-        {
-          "opt": "--blast",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Tabular BLAST file with COG IDs as subject."
-        },
-        {
-          "opt": "--cog",
-          "description": "If set, returns the COG ID, not the COG category."
-        },
-        {
-          "opt": "--desc",
-          "description": "Includes COG description (requires --cog)."
-        },
-        {
-          "opt": "--noverbose",
-          "description": "Run quietly, but show warnings."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "name": "COG Blast",
-          "mandatory": true,
-          "description": "Tabular BLAST with COG ID's or categories as subject."
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.filter.pl",
-      "description": ["Extracts a subset of hits (queries or subjects) from a",
-        "tabular BLAST."],
-      "help_arg": "",
-      "see_also": "BlastTab.subsample.pl",
-      "options": [
-        {
-          "name": "Subject",
-          "opt": "-s",
-          "description": ["If set, assumes that list.txt contains subject IDs.",
-            "By default: assumes query IDs."]
-        },
-        {
-          "name": "Inverse",
-          "opt": "-i",
-          "description": ["If set, reports the inverse of the list (i.e.,",
-            "reports only hits absent in the list)."]
-        },
-        {
-          "name": "list.txt",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "List of IDs to extract."
-        },
-        {
-          "name": "blast.txt",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Tabular BLAST file containing the superset of hits."
-        },
-        ">",
-        {
-          "name": "subset.txt",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Tabulat BLAST file to be created."
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.pairedHits.rb",
-      "description": "Identifies the best hits of paired-reads.",
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--blast",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input Tabular BLAST file.",
-          "note": ["This script assumes that paired hits are next to each",
-            "other. If this is not the case (e.g., because the blast was",
-            "concatenated), you must sort the input before running this",
-            "script."]
-        },
-        {
-          "name": "Min score",
-          "opt": "--minscore",
-          "arg": "float",
-          "default": 0.0,
-          "description": "Minimum (summed) Bit-Score to consider a pair-match."
-        },
-        {
-          "name": "Best hits",
-          "opt": "--besthits",
-          "arg": "integer",
-          "default": 0,
-          "description": ["Outputs top best-hits only (use 0 to output all the",
-            "paired hits)."]
-        },
-        {
-          "name": "Orientation",
-          "opt": "--orient",
-          "arg": "select",
-          "values": [0,1,2,3,4],
-          "default": 0,
-          "description": ["Checks the orientation of the hit. Values are: 0,",
-            "no checking; 1, same direction; 2, inwards; 3, outwards; 4,",
-            "different direction (i.e., 2 or 3)."]
-        },
-        {
-          "name": "Sister prefix",
-          "opt": "--sisprefix",
-          "arg": "string",
-          "default": "_",
-          "description": ["Sister read number prefix in the name of the reads.",
-            "Escape characters as dots (\\.), parenthesis (\\(, \\), \\[,",
-            "\\]), other characters with special meaning in regular",
-            "expressions (\\*, \\+, \\^, \\$, \\|). This prefix allows regular",
-            "expressions (for example, use ':|\\.' to use any of colon or",
-            "dot). Note that the prefix will not be included in the base name",
-            "reported in the output."]
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Tab-delimited flat file, with the following",
-            "columns: (1) Query ID (without the \"sister\" identifier). (2)",
-            "Subject ID. (3) Bit score (summed from both sister reads). (4/5)",
-            "From/To (subject) coordinates for read 1. (6/7) From/To (subject)",
-            "coordinates for read 2. (8) Reads orientation (1: same direction,",
-            "2: inwards, 3: outwards). (9) Estimated insert size."]
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.seqdepth.pl",
-      "description": "Estimates the sequencing depth of subject sequences.",
-      "help_arg": "",
-      "see_also": ["BlastTab.seqdepth_ZIP.pl", "BlastTab.seqdepth_nomedian.pl",
-        "BedGraph.tad.rb"],
-      "options": [
-        "cat",
-        {
-          "arg": "in_file",
-          "multiple_sep": " ",
-          "mandatory": true,
-          "description": ["One or more Tabular BLAST files of reads vs genes",
-            "(or contigs)."]
-        },
-        "|",
-        { "arg": "task" },
-        {
-          "name": "genes_or_ctgs.fna",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["A FastA file containing the genes or the contigs",
-            "(db)."]
-        },
-        ">",
-        {
-          "name": "genes_or_ctgs.cov",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["A tab-delimited file with the following columns:",
-            "(1) Subject ID. (2) Average sequencing depth. (3) Median",
-            "sequencing depth. (4) Number of mapped reads. (5) Length of the",
-            "subject sequence."]
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.seqdepth_ZIP.pl",
-      "description": ["Estimates the average sequencing depth of subject",
-        "sequences (genes or contigs) assuming a Zero-Inflated Poisson",
-        "distribution (ZIP) to correct for non-covered positions. It uses the",
-        "corrected method of moments estimators (CMMEs) as described by",
-        "Beckett et al [1]. Note that [1] has a mistake in eq. (2.4), that",
-        "should be: pi-hat-MM = 1 - (X-bar / lambda-hat-MM). Also note that a",
-        "more elaborated mixture distribution can arise from coverage",
-        "histograms (e.g., see [2] for an additional correction called 'tail",
-        "distribution' and mixtures involving negative binomial) so take these",
-        "results cum grano salis.\n [1]",
-        "http://anisette.ucs.louisiana.edu/Academic/Sciences/MATH/stage/stat2012.pdf\n",
-        "[2] Lindner et al, Bioinformatics, 2013."],
-      "help_arg": "",
-      "see_also": ["BlastTab.seqdepth.pl", "BlastTab.seqdepth_nomedian.pl",
-        "BedGraph.tad.rb"],
-      "options": [
-        "cat",
-        {
-          "name": "blast",
-          "arg": "in_file",
-          "multiple_sep": " ",
-          "mandatory": true,
-          "description": ["One or more Tabular BLAST files of reads vs genes",
-            "(or contigs)."]
-        },
-        "|",
-        { "arg": "task" },
-        {
-          "name": "genes_or_ctgs.fna",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["A FastA file containing the genes or the contigs",
-            "(db)."]
-        },
-        ">",
-        {
-          "name": "genes_or_ctgs.cov",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Output file with the following columns:",
-            "(1) Subject ID.",
-            "(2) Estimated average sequencing depth (CMME lambda).",
-            "(3) Zero-inflation (CMME pi).",
-            "(4) Observed average sequencing depth.",
-            "(5) Observed median sequencing depth.",
-            "(6) Observed median sequencing depth excluding zeroes.",
-            "(7) Number of mapped reads.",
-            "(8) Length of the subject sequence."]
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.seqdepth_nomedian.pl",
-      "description": ["Estimates the sequencing depth of subject",
-        "sequences. The values reported by this script may differ from those",
-        "of BlastTab.seqdepth.pl, because this script uses the aligned length",
-        "of the read while BlastTab.seqdepth.pl uses the aligned length of the",
-        "subject sequence."],
-      "help_arg": "",
-      "see_also": ["BlastTab.seqdepth.pl", "BlastTab.seqdepth_ZIP.pl"],
-      "options": [
-        "cat",
-        {
-          "arg": "in_file",
-          "multiple_sep": " ",
-          "mandatory": true,
-          "description": ["One or more Tabular BLAST files of reads vs genes",
-            "(or contigs)."]
-        },
-        "|",
-        { "arg": "task" },
-        {
-          "name": "genes_or_ctgs.fna",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["A FastA file containing the genes or the contigs",
-            "(db)."]
-        },
-        ">",
-        {
-          "name": "genes_or_ctgs.cov",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["A tab-delimited file with the following columns:",
-            "(1) Subject ID. (2) Average sequencing depth. (3) Number of",
-            "mapped reads. (4) Length of the subject sequence."]
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.subsample.pl",
-      "description": ["Filters a BLAST output including only the hits produced",
-        "by any of the given sequences as query."],
-      "help_arg": "",
-      "see_also": "BlastTab.filter.pl",
-      "options": [
-        {
-          "name": "blast.tab",
-          "mandatory": true,
-          "arg": "in_file",
-          "description": "BLAST output to be filtered (tabular format)."
-        },
-        {
-          "name": "sample.fa",
-          "mandatory": true,
-          "arg": "in_file",
-          "description": "Sequences to use as query (FastA format)."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "The filtered BLAST output (tabular format)."
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.sumPerHit.pl",
-      "description": ["Sums the weights of all the queries hitting each",
-        "subject. Often (but not necessarily) the BLAST files contain only",
-        "best matches. The weights can be any number, but a common use of this",
-        "Script is to add up counts (weights are integers). For example, in a",
-        "BLAST of predicted genes vs some annotation source, the weights could",
-        "be the number of reads recruited by each gene."],
-      "help_arg": "-h",
-      "options": [
-        {
-          "name": "Weights file",
-          "opt": "-w",
-          "arg": "in_file",
-          "description": ["A two-columns tab-delimited file containing the",
-            "the name (column 1) and the weight (column 2) of each query."]
-        },
-        {
-          "name": "Minimum score",
-          "opt": "-s",
-          "arg": "float",
-          "default": 0.0
-        },
-        {
-          "name": "Minimum identity (%)",
-          "opt": "-i",
-          "arg": "float",
-          "default": 0.0
-        },
-        {
-          "name": "Queries",
-          "opt": "-m",
-          "arg": "integer",
-          "default": 0,
-          "description": "Maximum number of queries. Set to 0 for all."
-        },
-        {
-          "name": "Normalize",
-          "opt": "-n",
-          "description": "Normalize weights by the number of hits per query."
-        },
-        {
-          "name": "Include zeroes",
-          "opt": "-z",
-          "description": ["Add zero when weight is not found (by default:",
-            "doesn't list them)."]
-        },
-        {
-          "name": "Run quietly",
-          "opt": "-q"
-        },
-        {
-          "name": "blast",
-          "arg": "in_file",
-          "multiple_sep": " ",
-          "mandatory": true,
-          "description": "One or more BLAST files."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["A two-columns tab-delimited file containing the",
-            "summed weights per hit."]
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.taxid2taxrank.pl",
-      "description": ["Takes a BLAST with NCBI Taxonomy IDs as subjects and",
-        "replaces them by names at a given taxonomic rank."],
-      "help_arg": "",
-      "options": [
-        {
-          "name": "tax_blast.txt",
-          "mandatory": true,
-          "arg": "in_file",
-          "description": ["BLAST output, where subject IDs are NCBI Taxonomy",
-            "IDs."]
-        },
-        {
-          "name": "nodes.dmp",
-          "mandatory": true,
-          "arg": "in_file",
-          "description": "Nodes file from NCBI Taxonomy.",
-          "source_url": "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"
-        },
-        {
-          "name": "names.dmp",
-          "mandatory": true,
-          "arg": "in_file",
-          "description": "Names file from NCBI Taxonomy.",
-          "source_url": "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz"
-        },
-        {
-          "name": "rank",
-          "arg": "string",
-          "mandatory": true,
-          "default": "genus",
-          "description": ["The rank to be reported. All the reported nodes",
-            "will have the same rank. To see supported values, run:\n",
-            "`cut -f 5 nodes.dmp | sort -u`."]
-        },
-        {
-          "name": "Best-hit",
-          "arg": "select",
-          "values": ["yes", "no"],
-          "default": "yes",
-          "description": ["Should it take into account the best hit per query",
-            "only? This is: should it filter by best-hit?"]
-        },
-        ">",
-        {
-          "name": "taxrank_list.txt",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["BLAST-like output, where subject IDs are Taxonomy",
-            "names."]
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.topHits_sorted.rb",
-      "description": "Reports the top-N best hits of a BLAST.",
-      "help_arg": "--help",
-      "see_also": "BlastTab.best_hit_sorted.pl",
-      "options": [
-        {
-          "name": "Sort",
-          "arg": "select",
-          "values": ["sort","cat"],
-          "mandatory": true,
-          "description": ["Use 'sort' if your BLAST is not pre-sorted by the",
-            "first column (or if you're not sure). Use 'cat' otherwise."]
-        },
-        {
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Tabular BLAST file."
-        },
-        "|",
-        { "arg": "task" },
-        "--blast",
-        "-",
-        {
-          "name": "Output",
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": [
-            "Output filtered BLAST file.",
-            "Supports compression with .gz extension."
-          ]
-        },
-        {
-          "opt": "--top",
-          "arg": "integer",
-          "default": 5,
-          "description": "Maximum number of hits to report for each query."
-        },
-        {
-          "opt": "--sort-by",
-          "arg": "select",
-          "values": ["bitscore", "evalue", "identity", "length", "no"],
-          "default": "bitscore",
-          "description": "Parameter used to detect the 'best' hits."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly."
-        }
-      ]
-    },
-    {
-      "task": "BlastTab.recplot2.R",
-      "description": ["Produce recruitment plot objects provided that",
-        "BlastTab.catsbj.pl has been previously executed."],
-      "help_arg": "--help",
-      "requires": [
-        { "r_package": "optparse" },
-        { "r_package": "enveomics.R" }
-      ],
-      "see_also": ["BlastTab.catsbj.pl", "GFF.catsbj.pl",
-        "RecPlot2.compareIdentities.R"],
-      "options": [
-        {
-          "opt": "--prefix",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Path to the prefix of the BlastTab.catsbj.pl output",
-            "files. At least the files .rec and .lim must exist with this",
-            "prefix."]
-        },
-        {
-          "opt": "--pos-breaks",
-          "arg": "integer",
-          "default": 1000,
-          "description": "Breaks in the positions histogram."
-        },
-        {
-          "opt": "--pos-breaks-tsv",
-          "arg": "in_file",
-          "description": ["File with (absolute) coordinates of breaks in the",
-            "position histogram."]
-        },
-        {
-          "opt": "--id-breaks",
-          "arg": "integer",
-          "default": 300,
-          "description": ["Breaks in the identity histogram."]
-        },
-        {
-          "opt": "--id-free-range",
-          "description": ["Indicates that the range should be freely set from",
-            "the observed values. Otherwise, 70-100% is included in the",
-            "identity histogram (default)."]
-        },
-        {
-          "opt": "--id-metric",
-          "arg": "select",
-          "values": ["identity", "corrected identity", "bit score"],
-          "default": "identity",
-          "description": ["Metric of identity to be used (Y-axis). Corrected",
-            "identity is only supported if the original BLAST file included",
-            "sequence lengths."]
-        },
-        {
-          "opt": "--id-summary",
-          "arg": "string",
-          "default": "sum",
-          "description": "Function summarizing the identity bins."
-        },
-        {
-          "opt": "--id-cutoff",
-          "arg": "float",
-          "default": 95.0,
-          "description": ["Cutoff of identity metric above which the hits are",
-            "considered 'in-group'. The 95% identity corresponds to the",
-            "expectation of ANI<95% within species."]
-        },
-        {
-          "opt": "--threads",
-          "arg": "integer",
-          "default": 2,
-          "description": "Number of threads to use."
-        },
-        {
-          "opt": "--no-verbose",
-          "description": "Indicates if the function should report the advance."
-        },
-        {
-          "opt": "--peaks-col",
-          "arg": "string",
-          "default": "NA",
-          "description": ["Color of peaks, mandatory for peak-finding (e.g.,",
-            "darkred)."]
-        },
-        {
-          "opt": "--peaks-method",
-          "arg": "select",
-          "values": ["emauto","em","mower"],
-          "default": "emauto",
-          "description": "Method to detect peaks."
-        },
-        {
-          "name": "R Object Output",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Recplo2 object that can be re-plotted using",
-            "R function plot."]
-        },
-        {
-          "name": "Graphical Output",
-          "arg": "out_file",
-          "description": "Recruitment plot in PDF."
-        },
-        {
-          "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)."
-        }
-      ]
-    },
-    {
-      "task": "RecPlot2.compareIdentities.R",
-      "description": ["Calculates the difference between identity",
-        "distributions of two recruitment plots."],
-      "help_arg": "--help",
-      "requires": [
-        { "r_package": "optparse" },
-        { "r_package": "enveomics.R" }
-      ],
-      "see_also": [ "BlastTab.recplot2.R" ],
-      "options": [
-        {
-          "opt": "--method",
-          "arg": "string",
-          "default": "hellinger",
-          "description": ["Distance method to use. This should be (an",
-            "unambiguous abbreviation of) one of:",
-            "'hellinger' (Hellinger, 1090, doi:10.1515/crll.1909.136.210),",
-            "'bhattacharyya' (Bhattacharyya, 1943, Bull. Calcutta Math. Soc.",
-            "35), 'kl' or 'kullback–leibler' (Kullback & Leibler, 1951,",
-            "doi:10.1214/aoms/1177729694), or 'euclidean'."]
-        },
-        {
-          "opt": "--pseudocounts",
-          "arg": "float",
-          "default": 0.0,
-          "description": ["Smoothing parameter for Laplace smoothing. Use 0",
-            "for no smoothing, or 1 for add-one smoothing."]
-        },
-        {
-          "opt": "--max-deviation",
-          "arg": "float",
-          "description": ["Maximum mean deviation between identity breaks",
-            "tolerated (as percent identity). Difference in number of",
-            "id.breaks is never tolerated."]
-        },
-        {
-          "arg": "in_file",
-          "name": "RecPlot A",
-          "mandatory": true,
-          "description": ["File containing the R object `rp` for the first",
-            "recruitment plot."]
-        },
-        {
-          "arg": "in_file",
-          "name": "RecPlot B",
-          "mandatory": true,
-          "description": ["File containing the R object `rp` for the second",
-            "recruitment plot."]
-        }
-      ]
-    }
-  ]
-}