Commit 35a30e14 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added a bit more docs to arg

parent b34b4b44
......@@ -30,7 +30,13 @@ object DownloadNcbiAssembly extends ToolCommand {
} text "where to write report from ncbi"
opt[String]("nameHeader") unbounded () valueName "<string>" action { (x, c) =>
c.copy(contigNameHeader = Some(x))
} text "What column to use from the NCBI report for the nam,e of the contigs"
} text
| What column to use from the NCBI report for the name of the contigs.
| All columns in the report can be used but this are the most common field to choose from:
| - 'Sequence-Name': Name of the contig within the assembly
| - 'UCSC-style-name': Name of the contig used by UCSC ( like hg19 )
| - 'RefSeq-Accn': Unique name of the contig at RefSeq (default for NCBI)""".stripMargin
opt[(String, String)]("mustHaveOne") unbounded () valueName "<column_name=regex>" action { (x, c) =>
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"
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