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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"name": "Reverse list",
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"opt": "-r",
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"description": "Extracts sequences NOT present in the list."
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"name": "Quiet",
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"description": "Runs quietly."
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"name": "List",
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"arg": "in_file",
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"mandatory": true,
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"description": "List of sequences to extract."
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"name": "Seqs.fq",
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"arg": "in_file",
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"mandatory": true,
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"description": "FastQ file containing the superset of sequences."
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"name": "Subset.fq",
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"arg": "out_file",
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"mandatory": true,
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"description": "FastQ file to be created."
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"task": "FastQ.interpose.pl",
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"description": ["Interposes sequences in FastQ format from two files",
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"into one output file. If more than two files are provided, the script",
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"will interpose all the input files."],
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"warn": ["Note that this script will check for the consistency of the",
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"names (assuming a pair of related reads contains the same name",
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"varying only in a trailing slash (/) followed by a digit. If you want",
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"to turn this feature off just set the -T option to zero. If you want",
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"to decrease the sampling period (to speed the script up) or increase",
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"it (to make it more sensitive to errors) just change -T option",
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"accordingly."],
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"see_also": ["FastQ.split.pl","FastA.interpose.pl"],
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"name": "Checking period",
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"default": 1000,
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"description": "Sampling period for names evaluation."
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"arg": "out_file",
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"mandatory": true,
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"description": "Output FastQ file."
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"arg": "in_file",
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"description": "First input FastQ file."
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"description": "Second input FastQ file."
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"arg": "in_file",
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"multiple_sep": " ",
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"description": "Any additional input FastQ files."
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"description": ["There are several FastQ formats. This script takes a",
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"negative values (the range of Solexa+64 is -5 to 40)."],
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"mandatory": true,
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"description": ["Output file in FastQ format with the specified",
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"description": "FastQ file containing the sequences."
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"description": "FastQ to create."
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"description": "Prefix to use in all IDs."
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"opt": "--suffix",
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"description": "Translates FastQ files into FastA.",
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"help_arg": "'' --help",
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"description": "Output FastA file."
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"description": ["Compares the estimated error of sequencing reads",
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"(Q-score) with observed mismatches (identity against a know",
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"name": "Tabular BLAST",
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"description": ["Tabular BLAST file mapping reads to reference",
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"description": "Output tab-delimited file to create."
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"name": "Input file",
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"opt": "--x",
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"arg": "in_file",
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"mandatory": true,
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"description": ["A tab-delimited file containing header (first row)",
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"and row names (first column)."]
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},
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{
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"opt": "--sizes",
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"arg": "string",
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"description": ["A numeric vector containing the real size of the",
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"the values are assumed to be 100%, otherwise the sum of the",
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"default": 9,
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"description": ["Number of categories in the first two saturation",
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"categories if needed."]
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"default": 4,
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"description": "Width of the barplot with respect to the legend."
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},
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"opt": "--legend-ncol",
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"default": 1,
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"description": "Number of columns in the legend."
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"opt": "--other-col",
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"description": "Color of the 'Others' category."
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"opt": "--add-trend",
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"description": ["Controls if semi-transparent areas are to be",
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"plotted between the bars to connect the regions (trend regions)."]
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"opt": "--organic-trend",
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"forces add.trend=TRUE."]
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},
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"opt": "--sort-by",
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"arg": "string",
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"default": "median",
|
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"description": ["Any function that takes a numeric vector and",
|
|
74
|
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"returns a numeric scalar. This function is applied to each row,",
|
|
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|
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"and the resulting values are used to sort the rows",
|
|
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|
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"(decreasingly). Good options include: sd, min, max, mean, median."]
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},
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|
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{
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|
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"opt": "--min-report",
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|
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"default": 101,
|
|
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|
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"description": ["Minimum percentage to report the value in the plot.",
|
|
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|
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"Any value above 100 indicates that no values are to be reported."]
|
|
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},
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"opt": "--order",
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"arg": "string",
|
|
88
|
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"description": ["Controls how the rows should be ordered. If empty",
|
|
89
|
+
"(default), sort.by is applied per row and the results are sorted",
|
|
90
|
+
"decreasingly. If NA, no sorting is performed, i.e., the original",
|
|
91
|
+
"order is respected. If a vector is provided, it is assumed to be",
|
|
92
|
+
"the custom order to be used (either by numeric index or by row",
|
|
93
|
+
"names). Separate values by commas."]
|
|
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|
+
},
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|
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|
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{
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|
96
|
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"opt": "--col",
|
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97
|
+
"arg": "string",
|
|
98
|
+
"description": ["Colors to use. If provided, overrides the variables",
|
|
99
|
+
"`top` and `colors.per.group`, but `other.col` is still used if",
|
|
100
|
+
"the vector is insufficient for all the rows. Separate values by",
|
|
101
101
|
"commas. An additional palette is available when using value",
|
|
102
102
|
"'coto' (palette contributed by Luis (Coto) Orellana)."]
|
|
103
|
-
|
|
104
|
-
|
|
105
|
-
|
|
106
|
-
|
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107
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120
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121
|
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122
|
-
|
|
103
|
+
},
|
|
104
|
+
{
|
|
105
|
+
"arg": "out_file",
|
|
106
|
+
"mandatory": true,
|
|
107
|
+
"description": "Output file in PDF format."
|
|
108
|
+
},
|
|
109
|
+
{
|
|
110
|
+
"name": "width",
|
|
111
|
+
"arg": "float",
|
|
112
|
+
"mandatory": true,
|
|
113
|
+
"default": 7,
|
|
114
|
+
"description": "Width of the plot (in inches)."
|
|
115
|
+
},
|
|
116
|
+
{
|
|
117
|
+
"name": "height",
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|
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|
+
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|
|
119
|
+
"mandatory": true,
|
|
120
|
+
"default": 7,
|
|
121
|
+
"description": "Height of the plot (in inches)."
|
|
122
|
+
}
|
|
123
123
|
]
|
|
124
124
|
}
|
|
125
125
|
]
|
|
@@ -0,0 +1,30 @@
|
|
|
1
|
+
{
|
|
2
|
+
"tasks": [
|
|
3
|
+
{
|
|
4
|
+
"task": "BedGraph.tad.rb",
|
|
5
|
+
"description": ["Estimates the truncated average sequencing depth (TAD)",
|
|
6
|
+
"from a BedGraph file."],
|
|
7
|
+
"warn": ["This script doesn't consider zero-coverage positions if",
|
|
8
|
+
"missing from the file. If you produce your BedGraph file with",
|
|
9
|
+
"bedtools genomecov and want to consider zero-coverage position, be",
|
|
10
|
+
"sure to use -bga (not -bg)."],
|
|
11
|
+
"see_also": ["BlastTab.seqdepth.pl", "BlastTab.seqdepth_ZIP.pl"],
|
|
12
|
+
"help_arg": "--help",
|
|
13
|
+
"options": [
|
|
14
|
+
{
|
|
15
|
+
"opt": "--input",
|
|
16
|
+
"arg": "in_file",
|
|
17
|
+
"mandatory": true,
|
|
18
|
+
"description": "Input BedGraph file."
|
|
19
|
+
},
|
|
20
|
+
{
|
|
21
|
+
"opt": "--range",
|
|
22
|
+
"arg": "float",
|
|
23
|
+
"default": 0.5,
|
|
24
|
+
"description": ["Central range to consider, between 0 and 1. By",
|
|
25
|
+
"default: inter-quartile range (0.5)."]
|
|
26
|
+
}
|
|
27
|
+
]
|
|
28
|
+
}
|
|
29
|
+
]
|
|
30
|
+
}
|