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biopet.biopet
Commits
912d98fe
Commit
912d98fe
authored
Nov 08, 2016
by
Peter van 't Hof
Browse files
Added all arg to centrifuge
parent
f25519d7
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/centrifuge/Centrifuge.scala
View file @
912d98fe
...
...
@@ -26,6 +26,50 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
@Output
(
doc
=
"Output with hits per sequence"
)
var
report
:
Option
[
File
]
=
None
@Output
(
required
=
false
)
var
un
:
Option
[
File
]
=
_
@Output
(
required
=
false
)
var
al
:
Option
[
File
]
=
_
@Output
(
required
=
false
)
var
unConc
:
Option
[
File
]
=
_
@Output
(
required
=
false
)
var
alConc
:
Option
[
File
]
=
_
@Output
(
required
=
false
)
var
metFile
:
Option
[
File
]
=
_
// Input args
var
q
:
Boolean
=
config
(
"q"
,
default
=
false
)
var
qseq
:
Boolean
=
config
(
"qseq"
,
default
=
false
)
var
f
:
Boolean
=
config
(
"f"
,
default
=
false
)
var
r
:
Boolean
=
config
(
"r"
,
default
=
false
)
var
c
:
Boolean
=
config
(
"c"
,
default
=
false
)
var
skip
:
Option
[
Int
]
=
config
(
"skip"
)
var
upto
:
Option
[
Int
]
=
config
(
"upto"
)
var
trim5
:
Option
[
Int
]
=
config
(
"trim5"
)
var
trim3
:
Option
[
Int
]
=
config
(
"trim3"
)
var
phred33
:
Boolean
=
config
(
"phred33"
,
default
=
false
)
var
phred64
:
Boolean
=
config
(
"phred64"
,
default
=
false
)
var
intQuals
:
Boolean
=
config
(
"int_quals"
,
default
=
false
)
var
ignoreQuals
:
Boolean
=
config
(
"ignore_quals"
,
default
=
false
)
var
nofw
:
Boolean
=
config
(
"nofw"
,
default
=
false
)
var
norc
:
Boolean
=
config
(
"norc"
,
default
=
false
)
// Classification args
var
minHitlen
=
Option
[
Int
]
=
config
(
"min_hitlen"
)
var
minTotallen
:
Option
[
Int
]
=
config
(
"min_totallen"
)
var
hostTaxids
:
List
[
Int
]
=
config
(
"host_taxids"
,
default
=
Nil
)
var
excludeTaxids
:
List
[
Int
]
=
config
(
"exclude_taxids"
,
default
=
Nil
)
// Output args
var
t
:
Boolean
=
config
(
"t"
,
default
=
false
)
var
quiet
:
Boolean
=
config
(
"quiet"
,
default
=
false
)
var
metStderr
:
Boolean
=
config
(
"met_stderr"
,
default
=
false
)
var
met
:
Option
[
Int
]
=
config
(
"met"
)
override
def
defaultThreads
=
8
executable
=
config
(
"exe"
,
default
=
"centrifuge"
,
freeVar
=
false
)
...
...
@@ -49,7 +93,34 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
* @return Command to run
*/
def
cmdLine
:
String
=
executable
+
//TODO: Options
conditional
(
q
,
"-q"
)
+
conditional
(
qseq
,
"--qseq"
)
+
conditional
(
f
,
"-f"
)
+
conditional
(
r
,
"-r"
)
+
conditional
(
c
,
"-c"
)
+
optional
(
"--skip"
,
skip
)
+
optional
(
"--upto"
,
upto
)
+
optional
(
"--trim5"
,
trim5
)
+
optional
(
"--trim3"
,
trim3
)
+
conditional
(
phred33
,
"--phred33"
)
+
conditional
(
phred64
,
"--phred64"
)
+
conditional
(
intQuals
,
"--int-quals"
)
+
conditional
(
ignoreQuals
,
"--ignore-quals"
)
+
conditional
(
nofw
,
"--nofw"
)
+
conditional
(
norc
,
"--norc"
)
+
optional
(
"--min-hitlen"
,
minHitlen
)
+
optional
(
"--min-totallen"
,
minTotallen
)
+
optional
(
"--host-taxids"
,
if
(
hostTaxids
.
nonEmpty
)
Some
(
hostTaxids
.
mkString
(
","
))
else
None
)
+
optional
(
"--exclude-taxids"
,
if
(
excludeTaxids
.
nonEmpty
)
Some
(
excludeTaxids
.
mkString
(
","
))
else
None
)
+
optional
(
"--met-file"
,
metFile
)
+
conditional
(
t
,
"-t"
)
+
conditional
(
quiet
,
"--quiet"
)
+
conditional
(
metStderr
,
"--met-stderr"
)
+
optional
(
"--met"
,
met
)
+
optional
(
if
(
un
.
exists
(
_
.
getName
.
endsWith
(
".gz"
)))
"--un-gz"
else
"--un"
,
un
)
+
optional
(
if
(
al
.
exists
(
_
.
getName
.
endsWith
(
".gz"
)))
"--al-gz"
else
"--al"
,
al
)
+
optional
(
if
(
unConc
.
exists
(
_
.
getName
.
endsWith
(
".gz"
)))
"--un-conc-gz"
else
"--un-conc"
,
unConc
)
+
optional
(
if
(
alConc
.
exists
(
_
.
getName
.
endsWith
(
".gz"
)))
"--al-conc-gz"
else
"--al-conc"
,
alConc
)
+
optional
(
"--threads"
,
threads
)
+
required
(
"-x"
,
index
)
+
(
inputR2
match
{
...
...
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