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biopet.biopet
Commits
35a30e14
Commit
35a30e14
authored
Nov 21, 2016
by
Peter van 't Hof
Browse files
Added a bit more docs to arg
parent
b34b4b44
Changes
1
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
View file @
35a30e14
...
...
@@ -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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