Added explicit @ClassType annotations to @Argument for Option[Int] or Option[Double] since scala seems to change the reflected type to Option[Object] on some systems.

Changed ReflectionUtils.getGenericTypes' order of looking for @ClassType since the primitive generic wasn't completely erased, only changed to Object which is incorrect.
More fixes to @Arguments labeled as java.io.File via incorrect @Input annotation.
Put in a default undocumented implementation of @Argument doc() to match the one added to @Input.

public/java/src/org/broadinstitute/sting/commandline/Argument.java

@@ -62,7 +62,7 @@ public @interface Argument {
      * --help argument is specified. 
      * @return Doc string associated with this command-line argument.
      */
-    String doc();
+    String doc() default "Undocumented option";
 
     /**
      * Is this argument required.  If true, the command-line argument system will

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala

@@ -27,28 +27,28 @@ class PacbioProcessingPipeline extends QScript {
   @Input(doc="dbsnp VCF file to use ", shortName="D", required=true)
   var dbSNP: File = _
 
-  @Input(doc="Number of jobs to scatter/gather. Default: 0." , shortName = "sg", required=false)
+  @Argument(doc="Number of jobs to scatter/gather. Default: 0." , shortName = "sg", required=false)
   var threads: Int = 0
 
-  @Input(doc="Sample Name to fill in the Read Group information (only necessary if using fasta/fastq)" , shortName = "sn", required=false)
+  @Argument(doc="Sample Name to fill in the Read Group information (only necessary if using fasta/fastq)" , shortName = "sn", required=false)
   var sample: String = "NA"
 
   @Input(doc="The path to the binary of bwa to align fasta/fastq files", fullName="path_to_bwa", shortName="bwa", required=false)
   var bwaPath: File = _
 
-  @Input(doc="Input is a BLASR generated BAM file", shortName = "blasr", fullName="blasr_bam", required=false)
+  @Argument(doc="Input is a BLASR generated BAM file", shortName = "blasr", fullName="blasr_bam", required=false)
   var BLASR_BAM: Boolean = false
 
   @Hidden
-  @Input(doc="The default base qualities to use before recalibration. Default is Q20 (should be good for every dataset)." , shortName = "dbq", required=false)
+  @Argument(doc="The default base qualities to use before recalibration. Default is Q20 (should be good for every dataset)." , shortName = "dbq", required=false)
   var dbq: Int = 20
 
   @Hidden
-  @Input(shortName="bwastring", required=false)
+  @Argument(shortName="bwastring", required=false)
   var bwastring: String = ""
 
   @Hidden
-  @Input(shortName = "test", fullName = "test_mode", required = false)
+  @Argument(shortName = "test", fullName = "test_mode", required = false)
   var testMode: Boolean = false
 
   val queueLogDir: String = ".qlog/"

public/scala/src/org/broadinstitute/sting/queue/QSettings.scala

@@ -25,7 +25,7 @@
 package org.broadinstitute.sting.queue
 
 import java.io.File
-import org.broadinstitute.sting.commandline.Argument
+import org.broadinstitute.sting.commandline.{ClassType, Argument}
 
 /**
  * Default settings settable on the command line and passed to CommandLineFunctions.
@@ -41,6 +41,7 @@ class QSettings {
   var jobQueue: String = _
 
   @Argument(fullName="job_priority", shortName="jobPriority", doc="Default priority for jobs. Min = 0, Max = 100", required=false)
+  @ClassType(classOf[Int])
   var jobPriority: Option[Int] = None
 
   @Argument(fullName="job_native_arg", shortName="jobNative", doc="Native arguments to pass to the job runner.", required=false)
@@ -53,15 +54,19 @@ class QSettings {
   var jobEnvironmentNames: Seq[String] = Nil
 
   @Argument(fullName="memory_limit", shortName="memLimit", doc="Default memory limit for jobs, in gigabytes. If not set defaults to 2GB.", required=false)
+  @ClassType(classOf[Double])
   var memoryLimit: Option[Double] = Some(2)
 
   @Argument(fullName="memory_limit_threshold", shortName="memLimitThresh", doc="After passing this threshold stop increasing memory limit for jobs, in gigabytes.", required=false)
+  @ClassType(classOf[Double])
   var memoryLimitThreshold: Option[Double] = None
 
   @Argument(fullName="resident_memory_limit", shortName="resMemLimit", doc="Default resident memory limit for jobs, in gigabytes.", required=false)
+  @ClassType(classOf[Double])
   var residentLimit: Option[Double] = None
 
   @Argument(fullName="resident_memory_request", shortName="resMemReq", doc="Default resident memory request for jobs, in gigabytes.", required=false)
+  @ClassType(classOf[Double])
   var residentRequest: Option[Double] = None
 
   @Argument(fullName="resident_memory_request_parameter", shortName="resMemReqParam", doc="Parameter for resident memory requests. By default not requested.", required=false)

public/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala

@@ -159,12 +159,11 @@ object ReflectionUtils {
   private def getGenericTypes(field: Field): Option[Array[Class[_]]] = {
     // TODO: Refactor: based on java code in org.broadinstitute.sting.commandline.ArgumentTypeDescriptor
     // If this is a parameterized collection, find the contained type.  If blow up if only one type exists.
-    if (field.getGenericType.isInstanceOf[ParameterizedType]) {
+    if (hasAnnotation(field, classOf[ClassType])) {
+      Some(Array(getAnnotation(field, classOf[ClassType]).value))
+    } else if (field.getGenericType.isInstanceOf[ParameterizedType]) {
       val parameterizedType = field.getGenericType.asInstanceOf[ParameterizedType]
       Some(parameterizedType.getActualTypeArguments.map(_.asInstanceOf[Class[_]]))
-    } else if (hasAnnotation(field, classOf[ClassType])) {
-      Some(Array(getAnnotation(field, classOf[ClassType]).value))
-    }
-    else None
+    } else None
   }
 }