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biopet.biopet
Commits
6b51387d
Commit
6b51387d
authored
Nov 23, 2016
by
Sander Bollen
Browse files
xhmm normalize wrapper
parent
aedc6bcd
Changes
1
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
0 → 100644
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6b51387d
package
nl.lumc.sasc.biopet.extensions.xhmm
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmNormalize
(
val
root
:
Configurable
)
extends
Xhmm
{
@Input
var
inputMatrix
:
File
=
_
@Input
var
pcaFile
:
File
=
_
@Output
var
normalizeOutput
:
File
=
_
@Argument
var
normalizeMethod
:
String
=
config
(
"normalize_method"
,
namespace
=
"xhmm"
,
default
=
"PVE_mean"
)
@Argument
var
pveFactor
:
Float
=
config
(
"pve_mean_factor"
,
namespace
=
"xhmm"
,
default
=
0.7
)
def
cmdLine
=
{
executable
+
required
(
"--normalize"
)
+
required
(
"-r"
,
inputMatrix
)
+
required
(
"--PCAfiles"
,
pcaFile
)
+
required
(
"--normalizeOutput"
,
normalizeOutput
)
+
required
(
"--PCnormalizeMethod"
,
normalizeMethod
)
+
required
(
"--PVE_mean_factor"
,
pveFactor
)
}
}
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