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biopet.biopet
Commits
e749d3ed
Commit
e749d3ed
authored
Sep 16, 2015
by
Peter van 't Hof
Browse files
Fix tool extensions
parent
48528ed5
Changes
21
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
View file @
e749d3ed
...
...
@@ -6,5 +6,12 @@ import nl.lumc.sasc.biopet.FullVersion
* Created by pjvanthof on 11/09/15.
*/
trait
ToolCommandFuntion
extends
BiopetJavaCommandLineFunction
{
def
toolObject
:
Object
override
def
getVersion
=
Some
(
"Biopet "
+
FullVersion
)
override
def
freezeFieldValues
()
:
Unit
=
{
javaMainClass
=
toolObject
.
getClass
.
getName
.
split
(
"$"
).
head
super
.
freezeFieldValues
()
}
}
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
View file @
e749d3ed
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
BastyGenerateFasta
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Reference
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BastyGenerateFasta
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BastyGenerateFasta
@Input
(
doc
=
"Input vcf file"
,
required
=
false
)
var
inputVcf
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala
View file @
e749d3ed
...
...
@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* @deprecated Use picard.util.BedToIntervalList instead
*/
class
BedToInterval
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedToInterval
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedToInterval
@Input
(
doc
=
"Input Bed file"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala
View file @
e749d3ed
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
BedtoolsCoverageToCounts
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedtoolsCoverageToCounts
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BedtoolsCoverageToCounts
@Input
(
doc
=
"Input fasta"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala
View file @
e749d3ed
...
...
@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
BiopetFlagstat
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Summarizable
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BiopetFlagstat
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BiopetFlagstat
@Input
(
doc
=
"Input bam"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala
View file @
e749d3ed
...
...
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* @param root Parent object
*/
class
FastqSplitter
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSplitter
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSplitter
@Input
(
doc
=
"Input fastq"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala
View file @
e749d3ed
...
...
@@ -32,7 +32,7 @@ import scala.util.matching.Regex
*/
class
FastqSync
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Summarizable
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSync
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSync
@Input
(
doc
=
"Original FASTQ file (read 1 or 2)"
,
shortName
=
"r"
,
required
=
true
)
var
refFastq
:
File
=
null
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala
View file @
e749d3ed
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
MergeAlleles
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeAlleles
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeAlleles
@Input
(
doc
=
"Input vcf files"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
List
[
File
]
=
Nil
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala
View file @
e749d3ed
...
...
@@ -30,7 +30,7 @@ import scala.collection.mutable.{ Set => MutSet }
*/
class
MergeTables
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeTables
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeTables
override
def
defaultCoreMemory
=
6.0
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
View file @
e749d3ed
...
...
@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import
scala.collection.JavaConversions._
class
MpileupToVcf
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Reference
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MpileupToVcf
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MpileupToVcf
@Input
(
doc
=
"Input mpileup file"
,
shortName
=
"mpileup"
,
required
=
false
)
var
inputMpileup
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala
View file @
e749d3ed
...
...
@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
* Created by pjvan_thof on 1/13/15.
*/
class
PrefixFastq
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
PrefixFastq
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
PrefixFastq
override
def
defaultCoreMemory
=
1.0
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala
View file @
e749d3ed
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
SageCountFastq
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCountFastq
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCountFastq
@Input
(
doc
=
"Input fasta"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala
View file @
e749d3ed
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
SageCreateLibrary
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateLibrary
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateLibrary
@Input
(
doc
=
"Input fasta"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala
View file @
e749d3ed
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
SageCreateTagCounts
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateTagCounts
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SageCreateTagCounts
@Input
(
doc
=
"Raw count file"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala
View file @
e749d3ed
...
...
@@ -14,7 +14,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
* @param root Configuration object for the pipeline
*/
class
SeqStat
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Summarizable
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SeqStat
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SeqStat
@Input
(
doc
=
"Input FASTQ"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
File
=
null
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala
View file @
e749d3ed
...
...
@@ -10,7 +10,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Created by pjvanthof on 22/08/15.
*/
class
SquishBed
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SquishBed
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
SquishBed
@Input
(
doc
=
"Input Bed file"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
View file @
e749d3ed
...
...
@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
VcfFilter
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfFilter
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfFilter
@Input
(
doc
=
"Input vcf"
,
shortName
=
"I"
,
required
=
true
)
var
inputVcf
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala
View file @
e749d3ed
...
...
@@ -30,7 +30,7 @@ import scala.io.Source
* Created by pjvan_thof on 1/10/15.
*/
class
VcfStats
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Summarizable
with
Reference
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfStats
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfStats
@Input
(
doc
=
"Input fastq"
,
shortName
=
"I"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala
View file @
e749d3ed
...
...
@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Biopet extension for tool VcfWithVcf
*/
class
VcfWithVcf
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfWithVcf
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfWithVcf
@Input
(
doc
=
"Input vcf file"
,
shortName
=
"input"
,
required
=
true
)
var
input
:
File
=
_
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala
View file @
e749d3ed
...
...
@@ -32,7 +32,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*/
class
VepNormalizer
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
javaMainClass
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VepNormalizer
.
getClass
.
getName
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VepNormalizer
@Input
(
doc
=
"Input VCF, may be indexed"
,
shortName
=
"InputFile"
,
required
=
true
)
var
inputVCF
:
File
=
null
...
...
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