Commit 5316c370 authored by bow's avatar bow

Update cuffquant wrapper with correct version exit codes

parent e2d73edf
......@@ -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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