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biopet.biopet
Commits
b220a035
Commit
b220a035
authored
Nov 24, 2016
by
Sander Bollen
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wrapper for xcnv to bed
parent
d64c43d1
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
...cala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
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biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
0 → 100644
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b220a035
package
nl.lumc.sasc.biopet.extensions.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommandFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Created by Sander Bollen on 24-11-16.
*/
class
XcnvToBed
(
val
root
:
Configurable
)
extends
ToolCommandFunction
{
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
XcnvToBed
@Input
var
inputXcnv
:
File
=
_
@Output
var
outpuBed
:
File
=
_
@Argument
var
sample
:
String
=
_
override
def
cmdLine
=
{
super
.
cmdLine
+
required
(
"-I"
,
inputXcnv
)
+
required
(
"-O"
,
outpuBed
)
+
required
(
"-S"
,
sample
)
}
}
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