miga-base 1.2.15.1 → 1.2.15.3

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

@@ -1,161 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "TRIBS.test.R",
-      "description": ["Estimates the empirical difference between all the",
-        "distances in a set of objects and a subset, together with its",
-        "statistical significance."],
-      "help_arg": "--help",
-      "requires": [
-        { "r_package": "optparse" },
-        { "r_package": "enveomics.R" }
-      ],
-      "see_also": ["TRIBS.plot-test.R"],
-      "options": [
-        {
-          "opt": "--dist",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "A tab-delimited matrix of distances."
-        },
-        {
-          "opt": "--selection",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "A list of names with the selection to evaluate."
-        },
-        {
-          "opt": "--replicates",
-          "arg": "integer",
-          "default": 1000,
-          "description": "Number of replications per point."
-        },
-        {
-          "opt": "--summary-fx",
-          "arg": "string",
-          "description": ["Function to summarize the distance distributions in",
-            "a given replicate. By default, the median distance is estimated."]
-        },
-        {
-          "opt": "--dist-method",
-          "arg": "string",
-          "default": "euclidean",
-          "description": ["Distance method between random points and samples",
-            "in the transformed space. See the R function 'dist'."]
-        },
-        {
-          "opt": "--dimensions",
-          "arg": "integer",
-          "description": ["Dimensions to use in the NMDS. By default, 5% of",
-            "the selection length."]
-        },
-        {
-          "opt": "--threads",
-          "arg": "integer",
-          "default": 2,
-          "description": "Number of threads to use."
-        },
-        {
-          "opt": "--verbosity",
-          "arg": "integer",
-          "default": 1,
-          "description": ["Verbosity. Use 0 to run quietly, increase for",
-            "additional information."]
-        },
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output file with the TRIBS test R object."
-        },
-        {
-          "name": "Bins",
-          "arg": "integer",
-          "default": 50,
-          "description": "Number of bins to evaluate in the range of distances."
-        }
-      ]
-    },
-    {
-      "task": "TRIBS.plot-test.R",
-      "description": "Plots an `enve.TRIBStest` object.",
-      "requires": [
-        { "r_package": "optparse" },
-        { "r_package": "enveomics.R" }
-      ],
-      "see_also": ["TRIBS.test.R"],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "Input TRIBS Test",
-          "opt": "--x",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "'enve.TRIBStest' object to plot."
-        },
-        {
-          "opt": "--type",
-          "arg": "select",
-          "values": ["overlap","difference"],
-          "default": "overlap",
-          "description": ["What to plot. 'overlap' generates a plot of the two",
-            "contrasting empirical PDFs (to compare against each other),",
-            "'difference' produces a plot of the differences between the",
-            "empirical PDFs (to compare against zero)."]
-        },
-        {
-          "opt": "--col",
-          "arg": "string",
-          "default": "#00000044",
-          "description": "Main color of the plot if type='difference'."
-        },
-        {
-          "opt": "--col1",
-          "arg": "string",
-          "description": ["First color of the plot if 'Type' is overlap. 'Col'",
-            "by default."]
-        },
-        {
-          "opt": "--col2",
-          "arg": "string",
-          "default": "#44001144",
-          "description": "Second color of the plot if 'Type' is overlap."
-        },
-        {
-          "opt": "--ylab",
-          "arg": "string",
-          "default": "Probability",
-          "description": "Y-axis label."
-        },
-        {
-          "opt": "--xlim",
-          "arg": "string",
-          "description": "X-axis limits, separate values by comma."
-        },
-        {
-          "opt": "--ylim",
-          "arg": "string",
-          "description": "Y-axis limits, separate values by comma."
-        },
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output file in PDF format."
-        },
-        {
-          "name": "Width",
-          "arg": "float",
-          "default": 7.0,
-          "mandatory": true,
-          "description": "Width of the plot in inches."
-        },
-        {
-          "name": "Height",
-          "arg": "float",
-          "default": 7.0,
-          "mandatory": true,
-          "description": "Height of the plot in inches."
-        }
-      ]
-    }
-  ]
-}