Commit d44f4f5d authored by Peter van 't Hof's avatar Peter van 't Hof

Added text to arguments

parent 91af94b8
...@@ -21,22 +21,22 @@ object DownloadNcbiAssembly extends ToolCommand { ...@@ -21,22 +21,22 @@ object DownloadNcbiAssembly extends ToolCommand {
class OptParser extends AbstractOptParser { class OptParser extends AbstractOptParser {
opt[String]('a', "assembly id") required () unbounded () valueName "<file>" action { (x, c) => opt[String]('a', "assembly id") required () unbounded () valueName "<file>" action { (x, c) =>
c.copy(assemblyId = x) c.copy(assemblyId = x)
} } text "refseq ID from NCBI"
opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) => opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) =>
c.copy(outputFile = x) c.copy(outputFile = x)
} } text "output Fasta file"
opt[File]("report") unbounded () valueName "<file>" action { (x, c) => opt[File]("report") unbounded () valueName "<file>" action { (x, c) =>
c.copy(reportFile = Some(x)) c.copy(reportFile = Some(x))
} } text "where to write report from ncbi"
opt[String]("nameHeader") unbounded () valueName "<string>" action { (x, c) => opt[String]("nameHeader") unbounded () valueName "<string>" action { (x, c) =>
c.copy(contigNameHeader = Some(x)) c.copy(contigNameHeader = Some(x))
} } text "What column to use from the NCBI report for the nam,e of the contigs"
opt[(String, String)]("mustHaveOne") unbounded () valueName "<string>" action { (x, c) => opt[(String, String)]("mustHaveOne") unbounded () valueName "<column_name=regex>" action { (x, c) =>
c.copy(mustHaveOne = (x._1, x._2) :: c.mustHaveOne) c.copy(mustHaveOne = (x._1, x._2) :: c.mustHaveOne)
} } text "This can be used to filter based on the NCBI report, multiple conditions can be given, at least 1 should be true"
opt[(String, String)]("mustNotHave") unbounded () valueName "<string>" action { (x, c) => opt[(String, String)]("mustNotHave") unbounded () valueName "<column_name=regex>" action { (x, c) =>
c.copy(mustNotHave = (x._1, x._2) :: c.mustNotHave) c.copy(mustNotHave = (x._1, x._2) :: c.mustNotHave)
} } text "This can be used to filter based on the NCBI report, multiple conditions can be given, all should be false"
} }
/** /**
......
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