Commit d399bdb3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed naming of sage tools

parent 06aa2313
......@@ -29,11 +29,10 @@ object BiopetExecutable {
nl.lumc.sasc.biopet.tools.BedToInterval,
nl.lumc.sasc.biopet.tools.MpileupToVcf,
nl.lumc.sasc.biopet.tools.FastqSplitter,
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts),
"sage" -> List(
nl.lumc.sasc.biopet.pipelines.sage.CreateTagCounts,
nl.lumc.sasc.biopet.pipelines.sage.CreateDeepsageLibrary,
nl.lumc.sasc.biopet.pipelines.sage.CountFastq)
nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts,
nl.lumc.sasc.biopet.pipelines.sage.SageCountFastq,
nl.lumc.sasc.biopet.pipelines.sage.SageCreateLibrary,
nl.lumc.sasc.biopet.pipelines.sage.SageCreateTagCounts)
)
/**
......
......@@ -65,7 +65,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
if (tagsLibrary == null) {
val cdl = new CreateDeepsageLibrary(this)
val cdl = new SageCreateLibrary(this)
cdl.input = transcriptome
cdl.output = outputDir + "taglib/tag.lib"
cdl.noAntiTagsOutput = outputDir + "taglib/no_antisense_genes.txt"
......@@ -182,12 +182,12 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
def addTablibCounts(fastq:File, outputPrefix: String, outputDir: String) {
val countFastq = new CountFastq(this)
val countFastq = new SageCountFastq(this)
countFastq.input = fastq
countFastq.output = outputDir + outputPrefix + ".raw.counts"
add(countFastq)
val createTagCounts = new CreateTagCounts(this)
val createTagCounts = new SageCreateTagCounts(this)
createTagCounts.input = countFastq.output
createTagCounts.tagLib = tagsLibrary
createTagCounts.countSense = outputDir + outputPrefix + ".tagcount.sense.counts"
......
......@@ -12,7 +12,7 @@ import scala.collection.SortedMap
import scala.collection.mutable.Map
import java.io.FileReader
class CountFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
class SageCountFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
@Input(doc = "Input fasta", shortName = "input", required = true)
......@@ -29,7 +29,7 @@ class CountFastq(val root: Configurable) extends BiopetJavaCommandLineFunction {
required("-o", output)
}
object CountFastq extends ToolCommand {
object SageCountFastq extends ToolCommand {
case class Args (input:File = null, output:File = null) extends AbstractArgs
class OptParser extends AbstractOptParser {
......
......@@ -13,7 +13,7 @@ import scala.collection.mutable.{Map, Set}
import scala.collection.JavaConversions._
import scala.util.matching.Regex
class CreateDeepsageLibrary(val root: Configurable) extends BiopetJavaCommandLineFunction {
class SageCreateLibrary(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
@Input(doc = "Input fasta", shortName = "input", required = true)
......@@ -46,7 +46,7 @@ class CreateDeepsageLibrary(val root: Configurable) extends BiopetJavaCommandLin
required("-o", output)
}
object CreateDeepsageLibrary extends ToolCommand {
object SageCreateLibrary extends ToolCommand {
case class Args (input:File = null, tag:String = "CATG", length:Int = 17,output:File = null, noTagsOutput:File = null,
noAntiTagsOutput:File = null, allGenesOutput:File = null) extends AbstractArgs
......
......@@ -10,7 +10,7 @@ import scala.io.Source
import scala.collection.mutable.Map
import scala.collection.SortedMap
class CreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineFunction {
class SageCreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineFunction {
javaMainClass = getClass.getName
@Input(doc = "Raw count file", shortName = "input", required = true)
......@@ -43,7 +43,7 @@ class CreateTagCounts(val root: Configurable) extends BiopetJavaCommandLineFunct
optional("--allantisense", countAllAntiSense)
}
object CreateTagCounts extends ToolCommand {
object SageCreateTagCounts extends ToolCommand {
case class Args (input:File = null, tagLib:File = null, countSense:File = null, countAllSense:File = null,
countAntiSense:File = null, countAllAntiSense:File = null) extends AbstractArgs
......
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