Commit edc81be3 authored by bow's avatar bow
Browse files

Merge branch 'fix-docs_tools' into 'develop'

Added text to args

Fixes #373 

See merge request !437
parents 7bb6eb02 9733edaf
......@@ -34,28 +34,28 @@ object VcfToTsv extends ToolCommand {
class OptParser extends AbstractOptParser {
opt[File]('I', "inputFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(inputFile = x)
}
} text "Input vcf file"
opt[File]('o', "outputFile") maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(outputFile = x)
} text "output file, default to stdout"
opt[String]('f', "field") unbounded () action { (x, c) =>
c.copy(fields = x :: c.fields)
}
} text "Genotype field to use" valueName "Genotype field name"
opt[String]('i', "info_field") unbounded () action { (x, c) =>
c.copy(infoFields = x :: c.infoFields)
}
} text "Info field to use" valueName "Info field name"
opt[Unit]("all_info") unbounded () action { (x, c) =>
c.copy(allInfo = true)
}
} text "Use all info fields in the vcf header"
opt[Unit]("all_format") unbounded () action { (x, c) =>
c.copy(allFormat = true)
}
} text "Use all genotype fields in the vcf header"
opt[String]('s', "sample_field") unbounded () action { (x, c) =>
c.copy(sampleFields = x :: c.sampleFields)
}
} text "Genotype fields to use in the tsv file"
opt[Unit]('d', "disable_defaults") unbounded () action { (x, c) =>
c.copy(disableDefaults = true)
}
} text "Don't output the default columns from the vcf file"
opt[String]("separator") maxOccurs 1 action { (x, c) =>
c.copy(separator = x)
} text "Optional separator. Default is tab-delimited"
......
......@@ -27,7 +27,7 @@ Usage: SamplesTsvToJson [options]
~~~
A user provides a TAB seperated file (TSV) with sample specific properties which are parsed into JSON format by the tool.
A user provides a TAB separated file (TSV) with sample specific properties which are parsed into JSON format by the tool.
For example, a user wants to add certain properties to the description of a sample, such as the treatment a sample received. Then a TSV file with an extra column called treatment is provided.
The resulting JSON file will have the 'treatment' property in it as well. The order of the columns is not relevant to the end result
......
......@@ -14,26 +14,33 @@ biopet tool VcfToTsv -h
Usage: VcfToTsv [options]
-l <value> | --log_level <value>
Log level
Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
-h | --help
Print usage
-v | --version
Print version
-I <file> | --inputFile <file>
Input vcf file
-o <file> | --outputFile <file>
output file, default to stdout
-f <value> | --field <value>
-i <value> | --info_field <value>
-f Genotype field name | --field Genotype field name
Genotype field to use
-i Info field name | --info_field Info field name
Info field to use
--all_info
Use all info fields in the vcf header
--all_format
Use all genotype fields in the vcf header
-s <value> | --sample_field <value>
Genotype fields to use in the tsv file
-d | --disable_defaults
Don't output the default columns from the vcf file
--separator <value>
Optional separator. Default is tab-delimited
--list_separator <value>
Optional list separator. By default, lists are separated by a comma
--max_decimals <value>
Number of decimal places for numbers. Default is 2
~~~
To run the tool:
......
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