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biopet.biopet
Commits
5316c370
Commit
5316c370
authored
Feb 18, 2015
by
bow
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Update cuffquant wrapper with correct version exit codes
parent
e2d73edf
Changes
1
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32 additions
and
31 deletions
+32
-31
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
+32
-31
No files found.
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala
View file @
5316c370
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Wrapper for the cuffquant command line tool.
...
...
@@ -31,10 +31,11 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction {
executable
=
config
(
"exe"
,
default
=
"cuffquant"
)
/** input file */
@Input
(
doc
=
"Input file (SAM or BAM)"
,
required
=
true
)
// in cuffquant this input: sample1_rep1.sam,sample1_rep2.sam sample2_rep1.sam,sample2_rep2.sam
// means we have 2 samples, each with 2 replicates
// so our input is a list of lists of Files
@Input
(
doc
=
"Input file (SAM or BAM)"
,
required
=
true
)
/*
in cuffquant this input: sample1_rep1.sam,sample1_rep2.sam sample2_rep1.sam,sample2_rep2.sam
means we have 2 samples, each with 2 replicates
so our input is a list of lists of Files
*/
var
input
:
List
[
List
[
File
]]
=
List
.
empty
[
List
[
File
]]
/** input GTF file */
...
...
@@ -118,32 +119,32 @@ class Cuffquant(val root: Configurable) extends BiopetCommandLineFunction {
override
val
versionRegex
=
"""cuffquant v(.*)"""
.
r
override
def
versionCommand
=
executable
override
val
versionExitcode
=
List
(
0
,
1
)
def
cmdLine
=
{
def
cmdLine
=
required
(
executable
)
+
required
(
"--output-dir"
,
output_dir
)
+
optional
(
"--mask-file"
,
mask_file
)
+
optional
(
"--frag-bias-correct"
,
frag_bias_correct
)
+
conditional
(
multi_read_correct
,
"--multi-read-correct"
)
+
optional
(
"--num-threads"
,
num_threads
)
+
optional
(
"--library-type"
,
library_type
)
+
optional
(
"--frag-len-mean"
,
frag_len_mean
)
+
optional
(
"--frag-len-std-dev"
,
frag_len_std_dev
)
+
optional
(
"--min-alignment-count"
,
min_alignment_count
)
+
optional
(
"--max-mle-iterations"
,
max_mle_iterations
)
+
conditional
(
verbose
,
"--verbose"
)
+
conditional
(
quiet
,
"--quiet"
)
+
optional
(
"--seed"
,
seed
)
+
conditional
(
no_update_check
,
"--no-update-check"
)
+
optional
(
"--max-bundle-frags"
,
max_bundle_frags
)
+
optional
(
"--max-frag-multihits"
,
max_frag_multihits
)
+
conditional
(
no_effective_length_correction
,
"--no-effective-length-correction"
)
+
conditional
(
no_length_correction
,
"--no-length-correction"
)
+
optional
(
"--read-skip-fraction"
,
read_skip_fraction
)
+
conditional
(
no_read_pairs
,
"--no-read-pairs"
)
+
optional
(
"--trim-read-length"
,
trim_read_length
)
+
conditional
(
no_scv_correction
,
"--no-scv-correction"
)
+
required
(
transcripts_gtf
)
+
required
(
input
.
map
(
_
.
mkString
(
";"
).
mkString
(
" "
)))
}
required
(
"--output-dir"
,
output_dir
)
+
optional
(
"--mask-file"
,
mask_file
)
+
optional
(
"--frag-bias-correct"
,
frag_bias_correct
)
+
conditional
(
multi_read_correct
,
"--multi-read-correct"
)
+
optional
(
"--num-threads"
,
num_threads
)
+
optional
(
"--library-type"
,
library_type
)
+
optional
(
"--frag-len-mean"
,
frag_len_mean
)
+
optional
(
"--frag-len-std-dev"
,
frag_len_std_dev
)
+
optional
(
"--min-alignment-count"
,
min_alignment_count
)
+
optional
(
"--max-mle-iterations"
,
max_mle_iterations
)
+
conditional
(
verbose
,
"--verbose"
)
+
conditional
(
quiet
,
"--quiet"
)
+
optional
(
"--seed"
,
seed
)
+
conditional
(
no_update_check
,
"--no-update-check"
)
+
optional
(
"--max-bundle-frags"
,
max_bundle_frags
)
+
optional
(
"--max-frag-multihits"
,
max_frag_multihits
)
+
conditional
(
no_effective_length_correction
,
"--no-effective-length-correction"
)
+
conditional
(
no_length_correction
,
"--no-length-correction"
)
+
optional
(
"--read-skip-fraction"
,
read_skip_fraction
)
+
conditional
(
no_read_pairs
,
"--no-read-pairs"
)
+
optional
(
"--trim-read-length"
,
trim_read_length
)
+
conditional
(
no_scv_correction
,
"--no-scv-correction"
)
+
required
(
transcripts_gtf
)
+
required
(
input
.
map
(
_
.
mkString
(
";"
).
mkString
(
" "
)))
}
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