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biopet.biopet
Commits
250e63be
Commit
250e63be
authored
Jul 25, 2017
by
pjvan_thof
Browse files
Fixing arguments
parent
c913b602
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateAnnotation.scala
View file @
250e63be
...
...
@@ -31,16 +31,16 @@ object ValidateAnnotation extends ToolCommand {
gtfFiles
:
List
[
File
]
=
Nil
)
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'r'
,
"refflatFile"
)
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
File
](
'r'
,
"refflatFile"
)
unbounded
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
refflatFile
=
Some
(
x
))
}
text
"Refflat file to check"
opt
[
File
](
'g'
,
"gtfFile"
)
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
File
](
'g'
,
"gtfFile"
)
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
gtfFiles
=
x
::
c
.
gtfFiles
)
}
text
"Gtf files to check"
opt
[
File
](
'R'
,
"reference"
)
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
File
](
'R'
,
"reference"
)
unbounded
()
required
()
maxOccurs
1
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
reference
=
x
)
}
text
"Reference fasta to check vcf file against"
opt
[
Unit
](
"disableFail"
)
maxOccurs
1
valueName
"<file>"
action
{
(
_
,
c
)
=>
opt
[
Unit
](
"disableFail"
)
unbounded
()
maxOccurs
1
valueName
"<file>"
action
{
(
_
,
c
)
=>
c
.
copy
(
failOnError
=
false
)
}
text
"Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0"
}
...
...
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