miga-base 0.3.1.6 → 0.3.1.7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/actions/ncbi_get.rb +57 -42
- data/lib/miga/result/base.rb +7 -0
- data/lib/miga/result/dates.rb +42 -0
- data/lib/miga/result.rb +4 -0
- data/lib/miga/version.rb +1 -1
- data/scripts/essential_genes.bash +5 -4
- data/utils/enveomics/Makefile +1 -1
- data/utils/enveomics/Manifest/Tasks/aasubs.json +75 -75
- data/utils/enveomics/Manifest/Tasks/blasttab.json +194 -185
- data/utils/enveomics/Manifest/Tasks/distances.json +130 -130
- data/utils/enveomics/Manifest/Tasks/fasta.json +51 -3
- data/utils/enveomics/Manifest/Tasks/fastq.json +161 -126
- data/utils/enveomics/Manifest/Tasks/graphics.json +111 -111
- data/utils/enveomics/Manifest/Tasks/mapping.json +30 -0
- data/utils/enveomics/Manifest/Tasks/ogs.json +308 -265
- data/utils/enveomics/Manifest/Tasks/other.json +451 -449
- data/utils/enveomics/Manifest/Tasks/remote.json +1 -1
- data/utils/enveomics/Manifest/Tasks/sequence-identity.json +18 -10
- data/utils/enveomics/Manifest/Tasks/tables.json +250 -250
- data/utils/enveomics/Manifest/Tasks/trees.json +52 -52
- data/utils/enveomics/Manifest/Tasks/variants.json +4 -4
- data/utils/enveomics/Manifest/categories.json +12 -4
- data/utils/enveomics/Manifest/examples.json +1 -1
- data/utils/enveomics/Scripts/BedGraph.tad.rb +71 -0
- data/utils/enveomics/Scripts/BlastTab.recplot2.R +23 -22
- data/utils/enveomics/Scripts/FastA.split.rb +79 -0
- data/utils/enveomics/Scripts/FastQ.test-error.rb +81 -0
- data/utils/enveomics/Scripts/JPlace.to_iToL.rb +272 -258
- data/utils/enveomics/Scripts/aai.rb +13 -6
- data/utils/enveomics/Scripts/ani.rb +2 -2
- data/utils/enveomics/Scripts/clust.rand.rb +102 -0
- data/utils/enveomics/Scripts/lib/enveomics_rb/enveomics.rb +12 -14
- data/utils/enveomics/Scripts/lib/enveomics_rb/jplace.rb +2 -2
- data/utils/enveomics/Scripts/rbm.rb +23 -14
- data/utils/enveomics/enveomics.R/DESCRIPTION +1 -1
- data/utils/enveomics/enveomics.R/R/barplot.R +2 -2
- metadata +9 -2
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"mandatory": true,
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"description": ["Input file containing the OGs (as generated by",
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"ogs.mcl.rb)."]
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"name": "Output file",
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"arg": "out_file",
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"mandatory": true,
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"description": "Output file containing the annotated OGs."
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"name": "Annotations",
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"arg": "in_file",
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"multiple_sep": ",",
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"description": ["Input file(s) containing the annotations. One or",
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"more tab-delimited files with the gene names in the first column",
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"and the annotation in the second."]
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"opt": "--format",
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"arg": "string",
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"default": "(\\S+)\\.txt",
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"description": ["Format of the filenames for the annotation files,",
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"using regex syntax."]
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"help_arg": "--help",
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"see_also": ["ogs.mcl.rb"],
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"opt": "--ogs",
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"description": "Input file containing the precomputed OGs."
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"description": "Output file in JSON format."
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"description": "Number of replicates to estimate.",
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"see_also": ["ogs.mcl.rb"],
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"description": "Output directory where to place extracted sequences."
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"name": "Sequences",
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"description": ["Path to the proteomes in FastA format, using '%s'",
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"opt": "--core",
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"arg": "float",
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"description": ["Use only OGs present in at least this fraction of",
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"the genomes. To use only the strict core genome*, use --core 1."],
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"note": ["* To use only the unus genome (OGs with exactly one gene",
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"per genome), use: --core 1 --duplicates 1."]
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"opt": "--duplicates",
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"description": ["Use only OGs with less than this number of",
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"in-paralogs in a genome. To use only genes without in-paralogs*,",
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"use --duplicates 1."],
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"note": ["* To use only the unus genome (OGs with exactly one gene",
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"per genome), use: --core 1 --duplicates 1."]
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"opt": "--per-genome",
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"description": ["If set, the output is generated per genome. By",
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"default, the output is per OG."]
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"description": ["If set, each sequence is prefixed with the genome",
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"name (or OG number, if --per-genome) and a dash."]
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"description": ["Get only one gene per genome per OG (random)",
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"regardless of in-paralogs. By default all genes are extracted."]
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"description": ["Get only one gene per genome per OG (first)",
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"description": "Output file containing the detected OGs."
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"cite": [
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["Hubert & Arabie, 1985, J Classif",
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|
|
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|
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|
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|
|
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|
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|
|
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|
+
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|
|
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|
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|
|
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|
+
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|
+
{
|
|
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|
+
"name": "Precision",
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|
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|
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|
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|
+
"arg": "integer",
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|
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|
+
"description": "Precision to report.",
|
|
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|
+
"default": 6
|
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|
+
},
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|
+
{
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|
+
"opt": "--quiet",
|
|
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|
+
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|
|
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|
+
}
|
|
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|
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|
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