miga-base 1.2.15.2 → 1.2.15.4

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

@@ -1,308 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "Table.df2dist.R",
-      "description": ["Transform a tab-delimited list of distances into a",
-        "squared matrix."],
-      "help_arg": "--help",
-      "requires": [ { "r_package": "optparse" } ],
-      "options": [
-        {
-          "name": "Input list",
-          "opt": "--x",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "A tab-delimited table with the distances."
-        },
-        {
-          "opt": "--obj1-index",
-          "arg": "integer",
-          "default": 1,
-          "description": ["Index of the column containing the ID of the object",
-            "1."]
-        },
-        {
-          "opt": "--obj2-index",
-          "arg": "integer",
-          "default": 2,
-          "description": ["Index of the column containing the ID of the object",
-            "2."]
-        },
-        {
-          "opt": "--dist-index",
-          "arg": "integer",
-          "default": 3,
-          "description": "Index of the column containing the distance."
-        },
-        {
-          "opt": "--default-d",
-          "arg": "integer",
-          "description": "Default value for missing values. NA if empty."
-        },
-        {
-          "opt": "--max-sim",
-          "arg": "float",
-          "description": ["If not-empty, assumes that the values are",
-            "similarity (not distance) and this is the maximum similarity",
-            "(corresponding to distance 0). Applies transformation:",
-            "distance = (max.sim - values)/max.sim."]
-        },
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output squared matrix in tab-separated values format."
-        }
-      ]
-    },
-    {
-      "task": "Table.filter.pl",
-      "description": ["Extracts (and re-orders) a subset of rows from a raw",
-        "table."],
-      "help_arg": "",
-      "options": [
-        {
-          "name": "Key",
-          "opt": "-k",
-          "arg": "integer",
-          "default": 1,
-          "description": "Column of the table to use as key to filter."
-        },
-        {
-          "name": "Sep",
-          "opt": "-s",
-          "arg": "string",
-          "description": ["String to use as separation between rows. By",
-            "default, tabulation."]
-        },
-        {
-          "name": "Inverse",
-          "opt": "-i",
-          "description": ["If set, reports the inverse of the list (i.e.,",
-            "reports only rows absent in the list). Implies 'No re-order'."]
-        },
-        {
-          "name": "Header",
-          "opt": "-h",
-          "description": "Keep first row of the table (header) untouched."
-        },
-        {
-          "name": "No re-order",
-          "opt": "-n",
-          "description": ["The output has the same order of the table. By",
-            "default, it prints in the order of the list."]
-        },
-        {
-          "name": "List",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "List of IDs to extract."
-        },
-        {
-          "name": "Table",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Table file containing the superset."
-        },
-        ">",
-        {
-          "name": "Subset",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Table file to be created."
-        }
-      ]
-    },
-    {
-      "task": "Table.merge.pl",
-      "description": "Merges multiple (two-column) lists into one table.",
-      "see_also": ["Table.split.pl"],
-      "help_arg": "",
-      "options": [
-        {
-          "name": "Strings",
-          "opt": "-s",
-          "description": ["Values are read as Strings. By default, values are",
-            "read as numbers."]
-        },
-        {
-          "name": "Input delimiter",
-          "opt": "-i",
-          "arg": "string",
-          "description": "Input field-delimiter. By default, tabulation."
-        },
-        {
-          "name": "Output delimiter",
-          "opt": "-o",
-          "arg": "string",
-          "description": "Output field-delimiter. By default: tabulation."
-        },
-        {
-          "name": "No header",
-          "opt": "-n",
-          "description": ["By default, the header is determined by the file",
-            "names."]
-        },
-        {
-          "name": "Empty",
-          "opt": "-e",
-          "description": ["Default string when no value is found. By default,",
-            "the 'empty' value is 0 if values are numeric (i.e., unless -s is",
-            "set) or an empty string otherwise."]
-        },
-        {
-          "name": "Header",
-          "opt": "-h",
-          "arg": "string",
-          "default": "Tag",
-          "description": "Header of the first column, containing the IDs."
-        },
-        {
-          "name": "Header format",
-          "opt": "-H",
-          "arg": "string",
-          "default": "(?:.*/)?([^\\.]+)",
-          "description": ["Format of filenames capturing the column header in",
-            "the first capturing parenthesis. Non-capturing paretheses can be",
-            "defined as (?:...). By default: '(?:.*/)?([^\\.]+)', which",
-            "captures the part of the basename of the file before the first",
-            "dot (if any)."]
-        },
-        {
-          "name": "Rows to ignore",
-          "opt": "-r",
-          "arg": "integer",
-          "default": 0,
-          "description": "Number of leading rows to ignore in the input files."
-        },
-        {
-          "arg": "in_file",
-          "mandatory": true,
-          "multiple_sep": " ",
-          "description": "Input two-column lists."
-        },
-        ">",
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Merged table."
-        }
-      ]
-    },
-    {
-      "task": "Table.round.rb",
-      "description": "Rounds numbers in a table.",
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "Input file",
-          "opt": "--in",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input table."
-        },
-        {
-          "name": "Output file",
-          "opt": "--out",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": "Output table."
-        },
-        {
-          "name": "Decimals",
-          "opt": "--ndigits",
-          "arg": "integer",
-          "default": 0,
-          "description": "Number of decimal digits."
-        },
-        {
-          "opt": "--floor",
-          "description": ["Floors the values instead of rounding them. Ignores",
-            "'Decimals'."]
-        },
-        {
-          "opt": "--ceil",
-          "description": ["Ceils the values instead of rounding them. Ignores",
-            "'Decimals'."]
-        },
-        {
-          "opt": "--delimiter",
-          "arg": "string",
-          "description": "String delimiting columns. By default, tabulation."
-        }
-      ]
-    },
-    {
-      "task": "Table.split.pl",
-      "description": ["Split a file with multiple columns into multiple",
-        "two-columns lists."],
-      "see_also": ["Table.merge.pl"],
-      "help_arg": "",
-      "options": [
-        {
-          "name": "Input delimiter",
-          "opt": "-i",
-          "arg": "string",
-          "description": "Input field-delimiter. By default, tabulation."
-        },
-        {
-          "name": "Out prefix",
-          "opt": "-o",
-          "arg": "string",
-          "description": "Prefix of the output files."
-        },
-        {
-          "name": "Output directory",
-          "opt": "-d",
-          "arg": "out_dir",
-          "description": "Output directory."
-        },
-        {
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input table."
-        }
-      ]
-    },
-    {
-       "task": "Table.replace.rb",
-       "description": "Replace a field in a table using a mapping file.",
-       "help_arg": "--help",
-       "options": [
-         {
-           "opt": "--map",
-           "arg": "in_file",
-           "mandatory": true,
-           "description": "Mapping file with two columns (key and replacement)."
-         },
-         {
-           "opt": "--in",
-           "arg": "in_file",
-           "mandatory": true,
-           "description": "Input table."
-         },
-         {
-           "opt": "--out",
-           "arg": "out_file",
-           "mandatory": true,
-           "description": "Output table."
-         },
-         {
-           "opt": "--key",
-           "arg": "integer",
-           "default": 1,
-           "description": "Column to replace in Input table."
-         },
-         {
-           "opt": "--unknown",
-           "arg": "string",
-           "description": "String to use whenever the key is not found in Map."
-         },
-         {
-           "opt": "--delimiter",
-           "arg": "string",
-           "description": "String delimiting columns. By default, tabulation."
-         }
-      ]
-    }
-  ]
-}

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

@@ -1,68 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "Newick.autoprune.R",
-      "description": ["Automatically prunes a tree, to keep representatives of",
-        "each clade."],
-      "requires": [ { "r_package": "optparse" }, { "r_package": "ape" } ],
-      "cite": [["Paradis et al, 2004, Bioinf",
-        "http://dx.doi.org/10.1093/bioinformatics/btg412"]],
-      "help_arg": "--help",
-      "options": [
-        {
-          "name": "Input tree",
-          "opt": "--t",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "A tree to prune in Newick format."
-        },
-        {
-          "opt": "--dist-quantile",
-          "arg": "float",
-          "default": 0.25,
-          "description": "The quantile of edge lengths."
-        },
-        {
-          "opt": "--min_dist",
-          "arg": "float",
-          "description": ["The minimum distance to allow between two tips. If",
-            "not set, dist.quantile is used instead to calculate it."]
-        },
-        {
-          "opt": "--quiet",
-          "description": ["Boolean indicating if the function must run without",
-            "output."]
-        },
-        {
-          "opt": "--max_iters",
-          "arg": "integer",
-          "default": 1000,
-          "description": "Maximum number of iterations."
-        },
-        {
-          "opt": "--min_nodes_random",
-          "arg": "integer",
-          "default": 40000,
-          "description": ["Minimum number of nodes to trigger 'tip-pairs'",
-            "nodes sampling. This sampling is less reproducible and more",
-            "computationally expensive, but it's the only solution if the",
-            "cophenetic matrix exceeds 2^31-1 entries; above that, it cannot",
-            "be represented in R."]
-        },
-        {
-          "opt": "--random_nodes_frx",
-          "arg": "float",
-          "default": 1.0,
-          "description": ["Fraction of the nodes to be sampled if more than",
-            "'Min nodes random'."]
-        },
-        {
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["Output file in Newick format containing the pruned",
-            "tree."]
-        }
-      ]
-    }
-  ]
-}

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

@@ -1,111 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "VCF.SNPs.rb",
-      "description": ["Counts the number of Single-Nucleotide Polymorphisms",
-        "(SNPs) in a VCF file."],
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--input",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input file in Variant Call Format (VCF)."
-        },
-        {
-          "name": "Filtered VCF",
-          "opt": "--out",
-          "arg": "out_file",
-          "description": "Output (filtered) file in Variant Call Format (VCF)."
-        },
-        {
-          "name": "Min DP",
-          "opt": "--min-dp",
-          "arg": "integer",
-          "description": "Minimum number of reads covering the position.",
-          "default": 4
-        },
-        {
-          "name": "Max DP",
-          "opt": "--max-dp",
-          "arg": "integer",
-          "description": ["Maximum number of reads covering the position. By",
-            "default no limit."]
-        },
-        {
-          "name": "Min Ref-DP",
-          "opt": "--min-ref-dp",
-          "arg": "integer",
-          "description": "Minimum number of reads supporting the REF allele.",
-          "default": 2
-        },
-        {
-          "name": "Min Alt-DP",
-          "opt": "--min-alt-dp",
-          "arg": "integer",
-          "description": "Minimum number of reads supporting the ALT allele.",
-          "default": 2
-        },
-        {
-          "opt": "--min-quality",
-          "arg": "float",
-          "description": "Minimum quality of the position mapping.",
-          "default": 0.0
-        },
-        {
-          "opt": "--min-shannon",
-          "arg": "integer",
-          "description": "Minimum information content (in bits, from 0 to 1).",
-          "default": 0.0
-        },
-        {
-          "opt": "--indels",
-          "description": "Process indels."
-        }
-      ]
-    },
-    {
-      "task": "VCF.KaKs.rb",
-      "description": ["Estimates the Ka/Ks ratio from the SNPs in a VCF file.",
-        "Ka and Ks are corrected using pseudo-counts, but no corrections for",
-        "multiple substitutions are applied."],
-      "help_arg": "--help",
-      "see_also": ["VCF.SNPs.rb"],
-      "options": [
-        {
-          "opt": "--input",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input file in Variant Call Format (VCF)."
-        },
-        {
-          "opt": "--seqs",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Input gene sequences (nucleotides) in FastA format."
-        },
-        {
-          "name": "Synonymous fraction",
-          "opt": "--syn-frx",
-          "arg": "float",
-          "description": ["Fraction of synonymous substitutions. If passed,",
-            "the number of sites are estimated (not counted per gene),",
-            "speeding up the computation ~10X."]
-        },
-        {
-          "name": "Bacterial code synonymous fraction",
-          "opt": "--syn-bacterial-code",
-          "description": ["Sets the synonymous fraction to 0.760417,",
-            "approximately the proportion of synonymous substitutions in the",
-            "bacterial code."]
-        },
-        {
-          "opt": "--codon-file",
-          "arg": "out_file",
-          "description": ["Output file including the codons of substitution",
-            "variants."]
-        }
-      ]
-    }
-  ]
-}

data/utils/enveomics/Manifest/categories.json

@@ -1,165 +0,0 @@
-{
-  "categories": {
-    "Sequence similarity search": {
-      "Statistics": [
-        "BedGraph.tad.rb",
-        "BedGraph.window.rb",
-        "BlastPairwise.AAsubs.pl",
-        "BlastTab.advance.bash",
-        "BlastTab.recplot2.R",
-        "BlastTab.seqdepth.pl",
-        "BlastTab.seqdepth_nomedian.pl",
-        "BlastTab.seqdepth_ZIP.pl",
-        "BlastTab.sumPerHit.pl",
-        "FastQ.test-error.rb",
-        "RecPlot2.compareIdentities.R"
-      ],
-      "Manipulation": [
-        "BlastTab.addlen.rb",
-        "BlastTab.best_hit_sorted.pl",
-        "BlastTab.catsbj.pl",
-        "BlastTab.cogCat.rb",
-        "BlastTab.filter.pl",
-        "BlastTab.kegg_pep2path_rest.pl",
-        "BlastTab.pairedHits.rb",
-        "BlastTab.subsample.pl",
-        "BlastTab.taxid2taxrank.pl",
-        "BlastTab.topHits_sorted.rb",
-        "sam.filter.rb"
-      ],
-      "Execution": [
-        "aai.rb",
-        "ani.rb",
-        "anir.rb",
-        "HMM.haai.rb",
-        "rbm.rb"
-      ]
-    },
-    "Sequence analyses": {
-      "Statistics": [
-        "FastA.gc.pl",
-        "FastA.length.pl",
-        "FastA.N50.pl",
-        "FastA.qlen.pl",
-        "FastQ.test-error.rb"
-      ],
-      "Manipulation": [
-        "FastA.extract.rb",
-        "FastA.filter.pl",
-        "FastA.filterLen.pl",
-        "FastA.filterN.pl",
-        "FastA.fragment.rb",
-        "FastA.interpose.pl",
-        "FastA.mask.rb",
-        "FastA.per_file.pl",
-        "FastA.rename.pl",
-        "FastA.revcom.pl",
-        "FastA.sample.rb",
-        "FastA.slider.pl",
-        "FastA.split.pl",
-        "FastA.split.rb",
-        "FastA.subsample.pl",
-        "FastA.tag.rb",
-        "FastA.toFastQ.rb",
-        "FastA.wrap.rb",
-        "FastQ.filter.pl",
-        "FastQ.interpose.pl",
-        "FastQ.maskQual.rb",
-        "FastQ.offset.pl",
-        "FastQ.split.pl",
-        "FastQ.tag.rb",
-        "FastQ.toFastA.awk"
-      ]
-    },
-    "Diversity": {
-      "Community": [
-        "AlphaDiversity.pl",
-        "Chao1.pl",
-        "Table.barplot.R",
-        "Table.prefScore.R"
-      ],
-      "Population": [
-        "VCF.SNPs.rb",
-        "VCF.KaKs.rb",
-        "Table.prefScore.R"
-      ]
-    },
-    "Annotation": {
-      "Database mapping": [
-        "BlastTab.kegg_pep2path_rest.pl",
-        "BlastTab.taxid2taxrank.pl",
-        "EBIseq2tax.rb",
-        "NCBIacc2tax.rb",
-        "gi2tax.rb",
-        "M5nr.getSequences.rb",
-        "RefSeq.download.bash",
-        "SRA.download.bash"
-      ],
-      "Tables": [
-        "Table.barplot.R",
-        "GenBank.add_fields.rb",
-        "MyTaxa.fragsByTax.pl",
-        "Table.df2dist.R",
-        "Table.filter.pl",
-        "Table.merge.pl",
-        "Table.replace.rb",
-        "Table.round.rb",
-        "Table.split.pl"
-      ],
-      "Search": [
-        "HMM.essential.rb",
-        "HMM.haai.rb",
-        "HMMsearch.extractIds.rb",
-        "ogs.annotate.rb",
-        "ogs.core-pan.rb",
-        "ogs.extract.rb",
-        "ogs.mcl.rb",
-        "ogs.stats.rb",
-        "ogs.rb"
-      ]
-    },
-    "Other data": {
-      "Phylogenetic and other distances": [
-        "CharTable.classify.rb",
-        "JPlace.distances.rb",
-        "JPlace.to_iToL.rb",
-        "Newick.autoprune.R",
-        "TRIBS.test.R",
-        "TRIBS.plot-test.R",
-        "Table.df2dist.R"
-      ],
-      "Taxonomic": [
-        "CharTable.classify.rb",
-        "EBIseq2tax.rb",
-        "NCBIacc2tax.rb",
-        "Table.barplot.R",
-        "gi2tax.rb",
-        "MyTaxa.fragsByTax.pl",
-        "MyTaxa.seq-taxrank.rb",
-        "Taxonomy.silva2ncbi.rb"
-      ],
-      "Alignments": [
-        "AAsubs.log2ratio.rb",
-        "Aln.cat.rb",
-        "Aln.convert.pl",
-        "BlastPairwise.AAsubs.pl"
-      ],
-      "Clustering": [
-        "ogs.mcl.rb",
-        "clust.rand.rb"
-      ],
-      "Read recruitments": [
-        "anir.rb",
-        "BedGraph.tad.rb",
-        "BedGraph.window.rb",
-        "BlastTab.catsbj.pl",
-        "BlastTab.pairedHits.rb",
-        "BlastTab.recplot2.R",
-        "FastQ.test-error.rb",
-        "GFF.catsbj.pl",
-        "RecPlot2.compareIdentities.R",
-        "sam.filter.rb"
-      ]
-    }
-  }
-}