diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
index cb5bad4ae..cdfc329e8 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -83,10 +83,10 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
                     getShortFieldSetter());
     }
 
-    protected static final String REQUIRED_TEMPLATE = " + \" %1$s \" + %2$s.format(%3$s)";
-    protected static final String REPEAT_TEMPLATE = " + repeat(\" %1$s \", %3$s, format=formatValue(%2$s))";
-    protected static final String OPTIONAL_TEMPLATE = " + optional(\" %1$s \", %3$s, format=formatValue(%2$s))";
-    protected static final String FLAG_TEMPLATE = " + (if (%3$s) \" %1$s\" else \"\")";
+    protected static final String REQUIRED_TEMPLATE = " + required(\"%1$s\", %3$s, spaceSeparated=true, escape=true, format=%2$s)";
+    protected static final String REPEAT_TEMPLATE = " + repeat(\"%1$s\", %3$s, spaceSeparated=true, escape=true, format=%2$s)";
+    protected static final String OPTIONAL_TEMPLATE = " + optional(\"%1$s\", %3$s, spaceSeparated=true, escape=true, format=%2$s)";
+    protected static final String FLAG_TEMPLATE = " + conditional(%3$s, \"%1$s\", escape=true, format=%2$s)";
 
     public final String getCommandLineAddition() {
         return String.format(getCommandLineTemplate(), getCommandLineParam(), getCommandLineFormat(), getFieldName());
@@ -136,7 +136,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
                     new IntervalStringArgumentField(argumentDefinition));
 
         // ROD Bindings are set by the RodBindField
-        } else if (RodBindField.ROD_BIND_FIELD.equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
+        } else if (RodBindArgumentField.ROD_BIND_FIELD.equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
             // TODO: Once everyone is using @Allows and @Requires correctly, we can stop blindly allowing Triplets
             return Arrays.asList(new RodBindArgumentField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, Tribble.STANDARD_INDEX_EXTENSION));
             //return Collections.<ArgumentField>emptyList();
@@ -337,6 +337,8 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
 
     // Allows the user to specify the track name, track type, and the file.
     public static class RodBindArgumentField extends ArgumentDefinitionField {
+        public static final String ROD_BIND_FIELD = "rodBind";
+
         public RodBindArgumentField(ArgumentDefinition argumentDefinition) {
             super(argumentDefinition);
         }
@@ -344,7 +346,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
         @Override protected String getFieldType() { return "List[RodBind]"; }
         @Override protected String getDefaultValue() { return "Nil"; }
         @Override protected String getCommandLineTemplate() {
-            return " + repeat(\"\", %3$s, format=RodBind.formatCommandLine(\"%1$s\"))";
+            return " + repeat(\"%1$s\", %3$s, formatPrefix=RodBind.formatCommandLineParameter, spaceSeparated=true, escape=true, format=%2$s)";
         }
     }
 
@@ -358,11 +360,11 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
         @Override protected String getDefaultValue() { return argumentDefinition.isMultiValued ? "Nil" : "_"; }
         @Override protected String getCommandLineTemplate() {
             if (argumentDefinition.isMultiValued) {
-                return " + repeat(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
+                return " + repeat(\"%1$s\", %3$s, formatPrefix=TaggedFile.formatCommandLineParameter, spaceSeparated=true, escape=true, format=%2$s)";
             } else if (!argumentDefinition.required) {
-                return " + optional(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
+                return " + optional(TaggedFile.formatCommandLineParameter(\"%1$s\", %3$s), %3$s, spaceSeparated=true, escape=true, format=%2$s)";
             } else {
-                return " + TaggedFile.formatCommandLine(\"%1$s\")(\"\", %3$s, \"\")";
+                return " + required(TaggedFile.formatCommandLineParameter(\"%1$s\", %3$s), %3$s, spaceSeparated=true, escape=true, format=%2$s)";
             }
         }
     }
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
index 9578eda84..67010c4d5 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -374,6 +374,9 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
         if (isGather)
             importSet.add("import org.broadinstitute.sting.commandline.Gather");
 
+        // Needed for ShellUtils.escapeShellArgument()
+        importSet.add("import org.broadinstitute.sting.queue.util.ShellUtils");
+
         // Sort the imports so that the are always in the same order.
         List<String> sortedImports = new ArrayList<String>(importSet);
         Collections.sort(sortedImports);
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java
deleted file mode 100644
index baf083575..000000000
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/RodBindField.java
+++ /dev/null
@@ -1,129 +0,0 @@
-/*
- * Copyright (c) 2010, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.queue.extensions.gatk;
-
-import org.broadinstitute.sting.commandline.Input;
-import org.broadinstitute.sting.gatk.WalkerManager;
-import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
-import org.broadinstitute.sting.gatk.walkers.RMD;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-
-import java.io.File;
-import java.lang.annotation.Annotation;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Allows user to specify the rod file but locks in the track name and the track type.
- */
-public class RodBindField extends ArgumentField {
-    public static final String ROD_BIND_FIELD = "rodBind";
-
-    private final String trackName;
-    private final String typeName;
-    private final List<RodBindField> relatedFields;
-    private final boolean isRequired;
-
-    public RodBindField(String trackName, String typeName, List<RodBindField> relatedFields, boolean isRequired) {
-        this.trackName = trackName;
-        this.typeName = typeName;
-        this.relatedFields = relatedFields;
-        this.isRequired = isRequired;
-    }
-
-    @SuppressWarnings("unchecked")
-    @Override protected Class<? extends Annotation> getAnnotationIOClass() { return Input.class; }
-    @Override protected Class<?> getInnerType() { return File.class; }
-    @Override protected String getFullName() { return escape(getRawFieldName()); }
-    @Override protected String getFieldType() { return "File"; }
-    @Override protected String getDefaultValue() { return "_"; }
-    @Override protected String getRawFieldName() { return this.trackName + this.typeName; }
-    @Override protected String getDoc() { return escape(this.typeName + " " + this.trackName); }
-    @Override protected boolean isRequired() { return this.isRequired; }
-
-    @Override public String getCommandLineAddition() {
-        // TODO: Stop allowing the generic "rodBind" triplets to satisfy the requirement after @Requires are fixed.
-        return String.format(" + optional(\" -B:%s,%s \", %s)",
-        /*
-        return String.format(this.useOption()
-                ? " + optional(\" -B:%s,%s \", %s)"
-                : " + \" -B:%s,%s \" + %s",
-        */
-                this.trackName, this.typeName, getFieldName());
-    }
-
-    private boolean useOption() {
-        return !this.isRequired || (relatedFields.size() > 1);
-    }
-
-    @Override protected String getExclusiveOf() {
-        StringBuilder exclusiveOf = new StringBuilder();
-        // TODO: Stop allowing the generic "rodBind" triplets to satisfy the requirement after @Requires are fixed.
-        if (this.isRequired)
-            exclusiveOf.append(ROD_BIND_FIELD);
-        for (RodBindField relatedField: relatedFields)
-            if (relatedField != this) {
-                if (exclusiveOf.length() > 0)
-                    exclusiveOf.append(",");
-                exclusiveOf.append(relatedField.getFieldName());
-            }
-        return exclusiveOf.toString();
-    }
-//
-//    public static List<ArgumentField> getRodArguments(Class<? extends Walker> walkerClass, RMDTrackBuilder trackBuilder) {
-//        List<ArgumentField> argumentFields = new ArrayList<ArgumentField>();
-//
-//        List<RMD> requires = WalkerManager.getRequiredMetaData(walkerClass);
-//        List<RMD> allows = WalkerManager.getAllowsMetaData(walkerClass);
-//
-//        for (RMD required: requires) {
-//            List<RodBindField> fields = new ArrayList<RodBindField>();
-//            String trackName = required.name();
-//            if ("*".equals(trackName)) {
-//                // TODO: Add the field triplet for name=* after @Allows and @Requires are fixed on walkers
-//                //fields.add(new RodBindArgumentField(argumentDefinition, true));
-//            } else {
-//                for (String typeName: trackBuilder.getFeatureManager().getTrackRecordTypeNames(required.type()))
-//                    fields.add(new RodBindField(trackName, typeName, fields, true));
-//            }
-//            argumentFields.addAll(fields);
-//        }
-//
-//        for (RMD allowed: allows) {
-//            List<RodBindField> fields = new ArrayList<RodBindField>();
-//            String trackName = allowed.name();
-//            if ("*".equals(trackName)) {
-//                // TODO: Add the field triplet for name=* after @Allows and @Requires are fixed on walkers
-//                //fields.add(new RodBindArgumentField(argumentDefinition, false));
-//            } else {
-//                for (String typeName: trackBuilder.getFeatureManager().getTrackRecordTypeNames(allowed.type()))
-//                    fields.add(new RodBindField(trackName, typeName, fields, true));
-//            }
-//            argumentFields.addAll(fields);
-//        }
-//
-//        return argumentFields;
-//    }
-}
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
index 036a77b58..8c9063c29 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
@@ -314,7 +314,7 @@ class GATKResourcesBundle extends QScript {
 
   class MakeDBSNP129(@Input dbsnp: File, @Input ref: File, @Output dbsnp129: File) extends SelectVariants with UNIVERSAL_GATK_ARGS {
     this.variant = dbsnp
-    this.select ++= List("\"dbSNPBuildID <= 129\"")
+    this.select ++= List("dbSNPBuildID <= 129")
     this.reference_sequence = ref
     this.out = dbsnp129
   }
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
index da02c8ac5..c06601a2d 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
@@ -248,10 +248,10 @@ class MethodsDevelopmentCallingPipeline extends QScript {
     this.V = t.rawIndelVCF
     this.out = t.filteredIndelVCF
     this.filterName ++= List("IndelQD", "IndelReadPosRankSum", "IndelFS")
-    this.filterExpression ++= List("\"QD < 2.0\"", "\"ReadPosRankSum < -20.0\"", "\"FS > 200.0\"")
+    this.filterExpression ++= List("QD < 2.0", "ReadPosRankSum < -20.0", "FS > 200.0")
     if (t.nSamples >= 10) {
         this.filterName ++= List("IndelInbreedingCoeff")
-        this.filterExpression ++= List("\"InbreedingCoeff < -0.8\"")
+        this.filterExpression ++= List("InbreedingCoeff < -0.8")
     }
     this.analysisName = t.name + "_VF"
     this.jobName =  queueLogDir + t.name + ".indelfilter"
diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
index 9bddfd97c..2f4aea755 100644
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala
@@ -62,7 +62,7 @@ class ExampleUnifiedGenotyper extends QScript {
     variantFilter.variant = genotyper.out
     variantFilter.out = swapExt(qscript.bamFile, "bam", "filtered.vcf")
     variantFilter.filterName = filterNames
-    variantFilter.filterExpression = filterExpressions.map("\"" + _ + "\"")
+    variantFilter.filterExpression = filterExpressions
 
     evalFiltered.eval :+= variantFilter.out
     evalFiltered.out = swapExt(variantFilter.out, "vcf", "eval")
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala
index 9af4d9bcf..deb83bf5a 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala
@@ -28,21 +28,14 @@ object RodBind {
   def apply(trackName: String, trackType: String, file: File, tag: String) = new RodBind(trackName, trackType, file, tag)
   def apply(trackName: String, trackType: String, file: File) = new RodBind(trackName, trackType, file, null)
 
-  /**
-   * Formats the rod binding on the command line.
-   * Used for optional and repeat.
-   * @param cmdLineParam command line parameter, ex: -B
-   * @param prefix unused
-   * @param value RodBind to add.
-   * @param suffix unused
-   * @return The command line addition.
-   */
-  def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
+  def formatCommandLineParameter( cmdLineParam: String, value: Any ) = {
     value match {
       case rodBind: RodBind if (rodBind.tag != null) =>
-        " %s:%s,%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.tag, rodBind.getPath)
+        "%s:%s,%s,%s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.tag)
       case rodBind: RodBind =>
-        " %s:%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.getPath)
+        "%s:%s,%s".format(cmdLineParam, rodBind.trackName, rodBind.trackType)
+      case x =>
+        ""
     }
   }
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala
index 295199993..940985f92 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.queue.extensions.gatk
 
 import java.io.File
 import org.broadinstitute.sting.utils.io.FileExtension
+import org.broadinstitute.sting.queue.util.ShellUtils
 
 /**
  * Used to provide tagged -I input_file arguments to the GATK.
@@ -19,21 +20,14 @@ object TaggedFile {
   def apply(path: String, tag: String) = new TaggedFile(path, tag)
   def apply(file: File, tag: String) = new TaggedFile(file, tag)
 
-  /**
-   * Formats the rod binding on the command line.
-   * Used for optional and repeat.
-   * @param cmdLineParam command line parameter, ex: -I
-   * @param prefix unused
-   * @param value TaggedFile to add.
-   * @param suffix unused
-   * @return The command line addition.
-   */
-  def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
+  def formatCommandLineParameter(cmdLineParam: String, value: Any) = {
     value match {
       case taggedFile: TaggedFile if (taggedFile.tag != null) =>
-          " %s:%s %s".format(cmdLineParam, taggedFile.tag, taggedFile.getPath)
+        "%s:%s".format(cmdLineParam, taggedFile.tag)
       case file: File =>
-          " %s %s".format(cmdLineParam, file.getPath)
+        cmdLineParam
+      case x =>
+        ""
     }
   }
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala
index 5456ed02c..93735e4ac 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala
@@ -55,11 +55,11 @@ class AddOrReplaceReadGroups extends org.broadinstitute.sting.queue.function.Jav
   override def outputBam = output
   this.createIndex = Some(true)
   override def commandLine = super.commandLine +
-       " RGID=" + RGID +
-       " RGLB=" + RGLB +
-       " RGPL=" + RGPL +
-       " RGPU=" + RGPU +
-       " RGSM=" + RGSM +
-       conditionalParameter(RGCN != null && !RGCN.isEmpty, " RGCN=" + RGCN) +
-       conditionalParameter(RGDS != null && !RGDS.isEmpty, " RGDS=" + RGDS)
+                             required("RGID=" + RGID) +
+                             required("RGLB=" + RGLB) +
+                             required("RGPL=" + RGPL) +
+                             required("RGPU=" + RGPU) +
+                             required("RGSM=" + RGSM) +
+                             conditional(RGCN != null && !RGCN.isEmpty, "RGCN=" + RGCN) +
+                             conditional(RGDS != null && !RGDS.isEmpty, "RGDS=" + RGDS)
 }
\ No newline at end of file
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
index d44d5e004..d73c556af 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
@@ -47,10 +47,8 @@ class MarkDuplicates extends org.broadinstitute.sting.queue.function.JavaCommand
   this.sortOrder = null
   this.createIndex = Some(true)
   override def commandLine = super.commandLine +
-       " M=" + metrics +
-       conditionalParameter(REMOVE_DUPLICATES, " REMOVE_DUPLICATES=true") +
-       conditionalParameter(MAX_FILE_HANDLES_FOR_READ_ENDS_MAP > 0, " MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=" + MAX_FILE_HANDLES_FOR_READ_ENDS_MAP.toString) +
-       conditionalParameter(SORTING_COLLECTION_SIZE_RATIO > 0, " SORTING_COLLECTION_SIZE_RATIO=" + SORTING_COLLECTION_SIZE_RATIO.toString)
-
-
+                             required("M=" + metrics) +
+                             conditional(REMOVE_DUPLICATES, "REMOVE_DUPLICATES=true") +
+                             conditional(MAX_FILE_HANDLES_FOR_READ_ENDS_MAP > 0, "MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=" + MAX_FILE_HANDLES_FOR_READ_ENDS_MAP.toString) +
+                             conditional(SORTING_COLLECTION_SIZE_RATIO > 0, "SORTING_COLLECTION_SIZE_RATIO=" + SORTING_COLLECTION_SIZE_RATIO.toString)
 }
\ No newline at end of file
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala
index fd107890e..036932cc6 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala
@@ -44,9 +44,7 @@ class MergeSamFiles extends org.broadinstitute.sting.queue.function.JavaCommandL
   override def outputBam = output
   this.createIndex = Some(true)
   override def commandLine = super.commandLine +
-       conditionalParameter(MERGE_SEQUENCE_DICTIONARIES, " MERGE_SEQUENCE_DICTIONARIES=true") +
-       conditionalParameter(USE_THREADING, " USE_THREADING=true") +
-       conditionalParameter(COMMENT != null && !COMMENT.isEmpty, " COMMENT=" + COMMENT)
-
-
+                             conditional(MERGE_SEQUENCE_DICTIONARIES, "MERGE_SEQUENCE_DICTIONARIES=true") +
+                             conditional(USE_THREADING, "USE_THREADING=true") +
+                             conditional(COMMENT != null && !COMMENT.isEmpty, "COMMENT=" + COMMENT)
 }
\ No newline at end of file
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
index 427c09f82..76856dc36 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
@@ -48,14 +48,13 @@ trait PicardBamFunction extends JavaCommandLineFunction {
   protected def outputBam: File
 
   abstract override def commandLine = super.commandLine +
-    Array(
-      repeat(" INPUT=", inputBams),
-      " TMP_DIR=" + jobTempDir,
-      optional(" OUTPUT=", outputBam),
-      optional(" COMPRESSION_LEVEL=", compressionLevel),
-      optional(" VALIDATION_STRINGENCY=", validationStringency),
-      optional(" SO=", sortOrder),
-      optional(" MAX_RECORDS_IN_RAM=", maxRecordsInRam),
-      optional(" ASSUME_SORTED=", assumeSorted),
-      optional(" CREATE_INDEX=", createIndex)).mkString
+                                      repeat("INPUT=", inputBams, spaceSeparated=false) +
+                                      required("TMP_DIR=" + jobTempDir) +
+                                      optional("OUTPUT=", outputBam, spaceSeparated=false) +
+                                      optional("COMPRESSION_LEVEL=", compressionLevel, spaceSeparated=false) +
+                                      optional("VALIDATION_STRINGENCY=", validationStringency, spaceSeparated=false) +
+                                      optional("SO=", sortOrder, spaceSeparated=false) +
+                                      optional("MAX_RECORDS_IN_RAM=", maxRecordsInRam, spaceSeparated=false) +
+                                      optional("ASSUME_SORTED=", assumeSorted, spaceSeparated=false) +
+                                      optional("CREATE_INDEX=", createIndex, spaceSeparated=false)
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala
index 72489dc87..b1968bee5 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala
@@ -42,7 +42,7 @@ class ReorderSam extends org.broadinstitute.sting.queue.function.JavaCommandLine
   this.createIndex = Some(true)
   this.sortOrder = null
   override def commandLine = super.commandLine +
-    " REFERENCE=" + sortReference +
-    optional(" ALLOW_INCOMPLETE_DICT_CONCORDANCE=", ALLOW_INCOMPLETE_DICT_CONCORDANCE)
-    optional(" ALLOW_CONTIG_LENGTH_DISCORDANCE=", ALLOW_CONTIG_LENGTH_DISCORDANCE)
+                             required("REFERENCE=" + sortReference) +
+                             optional("ALLOW_INCOMPLETE_DICT_CONCORDANCE=", ALLOW_INCOMPLETE_DICT_CONCORDANCE, spaceSeparated=false)
+                             optional("ALLOW_CONTIG_LENGTH_DISCORDANCE=", ALLOW_CONTIG_LENGTH_DISCORDANCE, spaceSeparated=false)
 }
\ No newline at end of file
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
index 746ce609e..60d8bfaf8 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
@@ -52,10 +52,10 @@ class RevertSam extends org.broadinstitute.sting.queue.function.JavaCommandLineF
   override def outputBam = output
   this.createIndex = Some(true)
   override def commandLine = super.commandLine +
-       conditionalParameter(!restoreOriginalQualities, " RESTORE_ORIGINAL_QUALITIES=false") +
-       conditionalParameter(!removeDuplicateInformation, " REMOVE_DUPLICATE_INFORMATION=false") +
-       conditionalParameter(!removeAlignmentInformation, " REMOVE_ALIGNMENT_INFORMATION=false") +
-       conditionalParameter(!attributesToClear.isEmpty, repeat(" ATTRIBUTE_TO_CLEAR=", attributesToClear)) +
-       conditionalParameter(sampleAlias != null, " SAMPLE_ALIAS=" + sampleAlias) +
-       conditionalParameter(libraryName != null, " LIBRARY_NAME=" + libraryName)
+                             conditional(!restoreOriginalQualities, "RESTORE_ORIGINAL_QUALITIES=false") +
+                             conditional(!removeDuplicateInformation, "REMOVE_DUPLICATE_INFORMATION=false") +
+                             conditional(!removeAlignmentInformation, "REMOVE_ALIGNMENT_INFORMATION=false") +
+                             repeat("ATTRIBUTE_TO_CLEAR=", attributesToClear, spaceSeparated=false) +   // repeat() returns "" for null/empty list
+                             conditional(sampleAlias != null, "SAMPLE_ALIAS=" + sampleAlias) +
+                             conditional(libraryName != null, "LIBRARY_NAME=" + libraryName)
 }
\ No newline at end of file
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
index 3a4217e60..3eb4e8e06 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
@@ -61,17 +61,17 @@ class SamToFastq extends org.broadinstitute.sting.queue.function.JavaCommandLine
   this.sortOrder = null
 
   override def commandLine = super.commandLine +
-       " FASTQ=" + fastq +
-       optional(" SECOND_END_FASTQ=", secondEndFastQ) +
-       conditionalParameter(outputPerReadGroup, optional(" OUTPUT_PER_RG=", outputPerReadGroup)) +
-       optional(" OUTPUT_DIR=", outputDir) +
-       conditionalParameter(!reReverse, optional(" RE_REVERSE=", reReverse)) +
-       conditionalParameter(includeNonPFReads, optional(" INCLUDE_NON_PF_READS=", includeNonPFReads)) +
-       optional(" CLIPPING_ATTRIBUTE=", clippingAttribute) +
-       optional(" CLIPPING_ACTION=", clippingAction) +
-       conditionalParameter (readOneTrim >= 0, optional(" READ1_TRIM=", readOneTrim)) +
-       conditionalParameter (readOneMaxBasesToWrite >= 0, optional(" READ1_MAX_BASES_TO_WRITE=", readOneMaxBasesToWrite)) +
-       conditionalParameter (readTwoTrim >= 0, optional(" READ2_TRIM=", readTwoTrim)) +
-       conditionalParameter (readTwoMaxBasesToWrite >=0, optional(" READ2_MAX_BASES_TO_WRITE=", readTwoMaxBasesToWrite)) +
-       conditionalParameter (includeNonPrimaryAlignments, optional(" INCLUDE_NON_PRIMARY_ALIGNMENTS=", includeNonPrimaryAlignments))
+                             required("FASTQ=" + fastq) +
+                             optional("SECOND_END_FASTQ=", secondEndFastQ, spaceSeparated=false) +
+                             conditional(outputPerReadGroup, "OUTPUT_PER_RG=" + outputPerReadGroup) +
+                             optional("OUTPUT_DIR=", outputDir, spaceSeparated=false) +
+                             conditional(!reReverse, "RE_REVERSE=" + reReverse) +
+                             conditional(includeNonPFReads, "INCLUDE_NON_PF_READS=" + includeNonPFReads) +
+                             optional("CLIPPING_ATTRIBUTE=", clippingAttribute, spaceSeparated=false) +
+                             optional("CLIPPING_ACTION=", clippingAction, spaceSeparated=false) +
+                             conditional(readOneTrim >= 0, "READ1_TRIM=" + readOneTrim) +
+                             conditional(readOneMaxBasesToWrite >= 0, "READ1_MAX_BASES_TO_WRITE=" + readOneMaxBasesToWrite) +
+                             conditional(readTwoTrim >= 0, "READ2_TRIM=" + readTwoTrim) +
+                             conditional(readTwoMaxBasesToWrite >= 0, "READ2_MAX_BASES_TO_WRITE=" + readTwoMaxBasesToWrite) +
+                             conditional(includeNonPrimaryAlignments, "INCLUDE_NON_PRIMARY_ALIGNMENTS=" + includeNonPrimaryAlignments)
 }
\ No newline at end of file
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
index 2c8fbc6d9..030e4b07d 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
@@ -50,11 +50,11 @@ class ValidateSamFile extends org.broadinstitute.sting.queue.function.JavaComman
   override def inputBams = input
   override def outputBam = output
   override def commandLine = super.commandLine +
-       " MODE=" + MODE +
-       " MAX_OUTPUT=" + MAX_OUTPUT +
-       " MAX_OPEN_TEMP_FILES=" + MAX_OPEN_TEMP_FILES +
-       conditionalParameter(!VALIDATE_INDEX, " VALIDATE_INDEX=false") +
-       conditionalParameter(IGNORE_WARNINGS, " IGNORE_WARNINGS=true") +
-       conditionalParameter(IS_BISULFITE_SEQUENCED, " IS_BISULFITE_SEQUENCED=true") +
-       conditionalParameter(IGNORE != null && !IGNORE.isEmpty, repeat(" IGNORE=", IGNORE))
+                             required("MODE=" + MODE) +
+                             required("MAX_OUTPUT=" + MAX_OUTPUT) +
+                             required("MAX_OPEN_TEMP_FILES=" + MAX_OPEN_TEMP_FILES) +
+                             conditional(!VALIDATE_INDEX, "VALIDATE_INDEX=false") +
+                             conditional(IGNORE_WARNINGS, "IGNORE_WARNINGS=true") +
+                             conditional(IS_BISULFITE_SEQUENCED, "IS_BISULFITE_SEQUENCED=true") +
+                             repeat("IGNORE=", IGNORE, spaceSeparated=false)  // repeat() returns "" for null/empty list
 }
\ No newline at end of file
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala
index 801a152ec..83a03b904 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala
@@ -48,7 +48,10 @@ class SamtoolsIndexFunction extends SamtoolsCommandLineFunction {
       bamFileIndex = new File(bamFile.getPath + ".bai")
   }
 
-  def commandLine = "%s index %s %s".format(samtools, bamFile, bamFileIndex)
+  def commandLine = required(samtools) +
+                    required("index") +
+                    required(bamFile) +
+                    required(bamFileIndex)
 
   override def dotString = "Index: %s".format(bamFile.getName)
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala
index 2b864def6..aff9a25c0 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala
@@ -55,7 +55,9 @@ class SamtoolsMergeFunction extends SamtoolsCommandLineFunction {
       ))
   }
 
-  def commandLine = "%s merge%s %s%s".format(
-    samtools, optional(" -R ", region),
-    outputBam, repeat(" ", inputBams))
+  def commandLine = required(samtools) +
+                    required("merge") +
+                    optional("-R", region) +
+                    required(outputBam) +
+                    repeat(inputBams)
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
index 62f66ec06..259856c17 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
@@ -50,11 +50,14 @@ class SnpEff extends JavaCommandLineFunction {
   @Output(doc="snp eff output")
   var outVcf: File = _
 
-  override def commandLine = Array(
-    super.commandLine,
-    " eff",
-    if (verbose) " -v" else "",
-    optional(" -c ", config),
-    " -i vcf -o vcf %s %s > %s".format(genomeVersion, inVcf, outVcf)
-  ).mkString
+  override def commandLine = super.commandLine +
+                             required("eff") +
+                             conditional(verbose, "-v") +
+                             optional("-c", config) +
+                             required("-i", "vcf") +
+                             required("-o", "vcf") +
+                             required(genomeVersion) +
+                             required(inVcf) +
+                             required(">", escape=false) +
+                             required(outVcf)
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
index ff77503ac..b08832f22 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
@@ -110,61 +110,178 @@ trait CommandLineFunction extends QFunction with Logging {
   }
 
   /**
-   * Repeats parameters with a prefix/suffix if they are set otherwise returns "".
-   * Skips null, Nil, None.  Unwraps Some(x) to x.  Everything else is called with x.toString.
-   * @param prefix Command line prefix per parameter.
-   * @param params Traversable parameters.
-   * @param suffix Optional suffix per parameter.
-   * @param separator Optional separator per parameter.
-   * @param format Format function if the value has a value
-   * @return The generated string
+   * Safely construct a full required command-line argument with consistent quoting, whitespace separation, etc.
+   *
+   * @param prefix Prefix to insert before the argument value (eg., "-f")
+   * @param param The argument value itself
+   * @param suffix Suffix to append after the argument value
+   * @param spaceSeparated If true, insert a space between the prefix, param, and suffix
+   * @param escape If true, quote the generated argument to avoid interpretation by the shell
+   * @param format Format String used to convert param to a String
+   * @return The combined and formatted argument, surrounded by whitespace
    */
-  protected def repeat(prefix: String, params: Traversable[_], suffix: String = "", separator: String = "",
-                       format: (String, Any, String) => String = formatValue("%s")) =
-    if (params == null)
-      ""
-    else
-      params.filter(param => hasValue(param)).map(param => format(prefix, param, suffix)).mkString(separator)
+  protected def required( prefix: String, param: Any, suffix: String = "", spaceSeparated: Boolean = true,
+                          escape: Boolean = true, format: String = "%s" ): String = {
+    " %s ".format(formatArgument(prefix, param, suffix, spaceSeparated, escape, format))
+  }
 
   /**
-   * Returns parameter with a prefix/suffix if it is set otherwise returns "".
-   * Does not output null, Nil, None.  Unwraps Some(x) to x.  Everything else is called with x.toString.
-   * @param prefix Command line prefix per parameter.
-   * @param param Parameter to check for a value.
-   * @param suffix Optional suffix per parameter.
-   * @param format Format function if the value has a value
-   * @return The generated string
+   * Safely construct a one-token required command-line argument with quoting
+   *
+   * @param param The command-line argument value
+   * @return The argument value quoted and surrounded by whitespace
    */
-  protected def optional(prefix: String, param: Any, suffix: String = "",
-                         format: (String, Any, String) => String = formatValue("%s")) =
-    if (hasValue(param)) format(prefix, param, suffix) else ""
+  protected def required( param: Any ): String = {
+    required("", param)
+  }
 
   /**
-   * Returns "" if the value is null or an empty collection, otherwise return the value.toString.
-   * @param format Format string if the value has a value
-   * @param prefix Command line prefix per parameter.
-   * @param param Parameter to check for a value.
-   * @param suffix Optional suffix per parameter.
-   * @return "" if the value is null, or "" if the collection is empty, otherwise the value.toString.
+   * Safely construct a one-token required command-line argument, and specify whether you want quoting
+   *
+   * @param param The command-line argument value
+   * @param escape If true, quote the generated argument to avoid interpretation by the shell
+   * @return The argument value, quoted if quoting was requested, and surrounded by whitespace
    */
-  protected def formatValue(format: String)(prefix: String, param: Any, suffix: String): String =
-    if (CollectionUtils.isNullOrEmpty(param))
-      ""
-    else
-      prefix + (param match {
-        case Some(x) => format.format(x)
-        case x => format.format(x)
-      }) + suffix
+  protected def required( param: Any, escape: Boolean ): String = {
+    required("", param, escape=escape)
+  }
 
   /**
-   * Returns the parameter if the condition is true. Useful for long string of parameters
-   * @param condition the condition to validate
-   * @param param the string to be returned in case condition is true
-   * @return param if condition is true, "" otherwise
+   * Safely construct a full optional command-line argument with consistent quoting, whitespace separation, etc.
+   * If the argument has no value, returns an empty String.
+   *
+   * @param prefix Prefix to insert before the argument value (eg., "-f")
+   * @param param The argument value itself (if null/empty, the method returns empty String)
+   * @param suffix Suffix to append after the argument value
+   * @param spaceSeparated If true, insert a space between the prefix, param, and suffix
+   * @param escape If true, quote the generated argument to avoid interpretation by the shell
+   * @param format Format String used to convert param to a String
+   * @return The combined and formatted argument, surrounded by whitespace, or an empty String
+   *         if the argument has no value
    */
-  protected def conditionalParameter(condition: Boolean, param: String): String =
-    if (condition == true)
-      param
-    else
+  protected def optional( prefix: String, param: Any, suffix: String = "", spaceSeparated: Boolean = true,
+                          escape: Boolean = true, format: String = "%s" ): String = {
+    if ( hasValue(param) ) " %s ".format(formatArgument(prefix, param, suffix, spaceSeparated, escape, format)) else ""
+  }
+
+  /**
+   * Safely construct a one-token optional command-line argument with quoting.
+   * If the argument has no value, returns an empty String.
+   *
+   * @param param The command-line argument value
+   * @return The argument value quoted and surrounded by whitespace, or an empty String
+   *         if the argument has no value
+   */
+  protected def optional( param: Any ): String = {
+    optional("", param)
+  }
+
+  /**
+   * Safely construct a one-token conditional command-line argument. If the provided condition
+   * is false, an empty String is returned.
+   *
+   * @param condition The condition to check
+   * @param param The command-line argument value
+   * @param escape If true, quote the generated argument to avoid interpretation by the shell
+   * @param format Format String used to convert param to a String
+   * @return The command-line argument value, quoted if quoting was requested and surrounded
+   *         by whitespace, or an empty String if the argument has no value.
+   */
+  protected def conditional( condition: Boolean, param: Any, escape: Boolean = true, format: String = "%s" ): String = {
+    if ( condition ) {
+      " %s ".format(formatArgument("", param, "", false, escape, format))
+    }
+    else {
       ""
+    }
+  }
+
+  /**
+   * Safely construct a series of full command-line arguments with consistent quoting, whitespace separation, etc.
+   *
+   * Each argument value is preceded by a prefix/suffix if they are set. A function can be provided to vary
+   * each prefix for each argument value (eg., -f:tag1 file1 -f:tag2 file2) -- the default is to use
+   * the same prefix for all arguments.
+   *
+   * @param prefix Prefix to insert before each argument value (eg., "-f")
+   * @param params The collection of argument values
+   * @param suffix Suffix to append after each argument value
+   * @param separator Specifies how to separate the various arguments from each other
+   *                  (eg., what should go between '-f' 'file1' and '-f' 'file2'?)
+   *                  Default is one space character.
+   * @param spaceSeparated If true, insert a space between each individual prefix, param, and suffix
+   * @param escape If true, quote the generated argument to avoid interpretation by the shell
+   * @param format Format String used to convert each individual param within params to a String
+   * @param formatPrefix Function mapping (prefix, argumentValue) pairs to prefixes. Can be used to
+   *                     vary each prefix depending on the argument value (useful for tags, etc.).
+   *                     Default is to use the same prefix for all argument values.
+   * @return The series of command-line arguments, quoted and whitespace-delimited as requested,
+   *         or an empty String if params was null/Nil/None.
+   */
+  protected def repeat(prefix: String, params: Traversable[_], suffix: String = "", separator: String = " ",
+                       spaceSeparated: Boolean = true, escape: Boolean = true, format: String = "%s",
+                       formatPrefix: (String, Any) => String = (prefix, value) => prefix): String = {
+    if (CollectionUtils.isNullOrEmpty(params))
+      ""
+    else
+      " %s ".format(params.filter(param => hasValue(param)).map(param => formatArgument(formatPrefix(prefix, param), param, suffix, spaceSeparated, escape, format)).mkString(separator))
+  }
+
+  /**
+   * Safely construct a series of one-token command-line arguments with quoting and space separation.
+   *
+   * @param params The collection of argument values
+   * @return The argument values quoted and space-delimited, or an empty String if params was null/Nil/None
+   */
+  protected def repeat( params: Traversable[_] ): String = {
+    repeat("", params)
+  }
+
+  /**
+   * Given an (optional) prefix, an argument value, and an (optional) suffix, formats a command-line
+   * argument with the specified level of quoting and space-separation.
+   *
+   * Helper method for required(), optional(), conditional(), and repeat() -- do not use this
+   * method directly!
+   *
+   * @param prefix Prefix to insert before the argument value (eg., "-f"). Ignored if empty/null.
+   * @param param The argument value itself. If this is Some(x), it is unwrapped to x before processing.
+   * @param suffix Suffix to append after the argument value. Ignored if empty/null.
+   * @param spaceSeparated If true, insert a space between the prefix, param, and suffix
+   * @param escape If true, quote the generated argument to avoid interpretation by the shell
+   * @param paramFormat Format string used to convert param to a String
+   * @return The combined and formatted argument, NOT surrounded by any whitespace.
+   *         Returns an empty String if param was null/empty.
+   */
+  protected def formatArgument( prefix: String, param: Any, suffix: String, spaceSeparated: Boolean, escape: Boolean,
+                                paramFormat: String ): String = {
+    if (CollectionUtils.isNullOrEmpty(param)) {
+      return ""
+    }
+
+    // Trim leading and trailing whitespace off our three tokens, and unwrap Some(x) to x for the param
+    val trimmedValues : List[String] = List((if ( prefix != null ) prefix.trim else ""),
+                                            (param match {
+                                              case Some(x) => paramFormat.format(x).trim
+                                              case x => paramFormat.format(x).trim
+                                            }),
+                                            (if ( suffix != null ) suffix.trim else ""))
+    var joinedArgument : String = null
+
+    // If the user requested space-separation, join the tokens with a space, and escape individual
+    // NON-EMPTY tokens if escaping was requested (eg., ("-f", "foo", "") -> "'-f' 'foo'")
+    if ( spaceSeparated ) {
+      joinedArgument = trimmedValues.map(x => if ( x.length > 0 && escape ) ShellUtils.escapeShellArgument(x) else x).mkString(" ").trim()
+    }
+
+    // Otherwise join the tokens without any intervening whitespace, and if quoting was requested
+    // quote the entire concatenated value (eg., ("-Xmx", "4", "G") -> "'-Xmx4G'")
+    else  {
+      joinedArgument = if ( escape ) ShellUtils.escapeShellArgument(trimmedValues.mkString("")) else trimmedValues.mkString("")
+    }
+
+    // If the user requested escaping and we ended up with an empty String after joining, quote the empty
+    // String to preserve the command line token. Otherwise just return the joined argument
+    if ( joinedArgument.length == 0 && escape ) ShellUtils.escapeShellArgument(joinedArgument) else joinedArgument
+  }
 }
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala b/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
index 4a50a72ac..8cbc2c577 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
@@ -49,18 +49,6 @@ trait JavaCommandLineFunction extends CommandLineFunction {
    */
   var javaMemoryLimit: Option[Double] = None
 
-  /**
-   * Returns the java executable to run.
-   */
-  def javaExecutable: String = {
-    if (jarFile != null)
-      "-jar " + jarFile
-    else if (javaMainClass != null)
-      "-cp \"%s\" %s".format(javaClasspath.mkString(File.pathSeparator), javaMainClass)
-    else
-      null
-  }
-
   override def freezeFieldValues() {
     super.freezeFieldValues()
 
@@ -71,11 +59,25 @@ trait JavaCommandLineFunction extends CommandLineFunction {
       javaClasspath = JavaCommandLineFunction.currentClasspath
   }
 
-  def javaOpts = "%s -Djava.io.tmpdir=%s"
-    .format(optional(" -Xmx", javaMemoryLimit.map(gb => (gb * 1024).ceil.toInt), "m"), jobTempDir)
+  /**
+   * Returns the java executable to run.
+   */
+  def javaExecutable: String = {
+    if (jarFile != null)
+      required("-jar", jarFile)
+    else if (javaMainClass != null)
+      required("-cp", javaClasspath.mkString(File.pathSeparator)) +
+      required(javaMainClass)
+    else
+      null
+  }
 
-  def commandLine = "java%s %s"
-    .format(javaOpts, javaExecutable)
+  def javaOpts = required("-Xmx", javaMemoryLimit.map(gb => (gb * 1024).ceil.toInt), "m", spaceSeparated=false) +
+                 required("-Djava.io.tmpdir=", jobTempDir, spaceSeparated=false)
+
+  def commandLine = required("java") +
+                    javaOpts +
+                    javaExecutable
 }
 
 object JavaCommandLineFunction {
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/ShellUtils.scala b/public/scala/src/org/broadinstitute/sting/queue/util/ShellUtils.scala
new file mode 100644
index 000000000..3cb1a705a
--- /dev/null
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/ShellUtils.scala
@@ -0,0 +1,36 @@
+package org.broadinstitute.sting.queue.util
+
+import java.lang.IllegalArgumentException
+
+object ShellUtils {
+
+  /**
+   * Escapes the String it's passed so that it will be interpreted literally when
+   * parsed by sh/bash. Can correctly escape all characters except \0, \r, and \n
+   *
+   * Replaces all instances of ' with '\'', and then surrounds the resulting String
+   * with single quotes.
+   *
+   * Examples:
+   * ab   ->  'ab'
+   * a'b  ->  'a'\''b'
+   * ''   ->  ''\'''\'''
+   *
+   * Since \' is not supported inside single quotes in the shell (ie., '\'' does not work),
+   * whenever we encounter a single quote we need to terminate the existing single-quoted
+   * string, place the \' outside of single quotes, and then start a new single-quoted
+   * string. As long as we don't insert spaces between the separate strings, the shell will
+   * concatenate them together into a single argument value for us.
+   *
+   * @param str the String to escape
+   * @return the same String quoted so that it will be interpreted literally when
+   *         parsed by sh/bash
+   */
+  def escapeShellArgument ( str : String ) : String = {
+    if ( str == null ) {
+      throw new IllegalArgumentException("escapeShellArgument() was passed a null String")
+    }
+
+    "'" + str.replaceAll("'", "'\\\\''") + "'"
+  }
+}
\ No newline at end of file
diff --git a/public/scala/test/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala b/public/scala/test/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala
new file mode 100644
index 000000000..eb50c3a2e
--- /dev/null
+++ b/public/scala/test/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala
@@ -0,0 +1,171 @@
+package org.broadinstitute.sting.queue.function
+
+import org.testng.Assert
+import org.testng.annotations.{DataProvider, Test}
+
+// Since "protected" in Scala is subclass-only and doesn't allow package-level access, we need to
+// extend a class if we want to test it
+class CommandLineFunctionUnitTest extends CommandLineFunction {
+  def commandLine = ""
+
+  @DataProvider( name="formatArgumentTestData" )
+  def formatArgumentDataProvider = {
+    Array(Array("", "argvalue", "", true, true, "'argvalue'"),
+          Array("", "argvalue", "", true, false, "argvalue"),
+          Array("", "argvalue", "", false, true, "'argvalue'"),
+          Array("", "argvalue", "", false, false, "argvalue"),
+          Array("-arg", "argvalue", "", true, true, "'-arg' 'argvalue'"),
+          Array("-arg", "argvalue", "", true, false, "-arg argvalue"),
+          Array("ARGNAME=", "ARGVALUE", "", false, true, "'ARGNAME=ARGVALUE'"),
+          Array("ARGNAME=", "ARGVALUE", "", false, false, "ARGNAME=ARGVALUE"),
+          Array("-Xmx", "4", "G", true, true, "'-Xmx' '4' 'G'"),
+          Array("-Xmx", "4", "G", true, false, "-Xmx 4 G"),
+          Array("-Xmx", "4", "G", false, true, "'-Xmx4G'"),
+          Array("-Xmx", "4", "G", false, false, "-Xmx4G"),
+          Array("", "", "", true, true, "''"),
+          Array("", "", "", true, false, ""),
+          Array("", "", "", false, true, "''"),
+          Array("", "", "", false, false, ""),
+          Array("", null, "", true, true, ""),
+          Array("", Nil, "", true, true, ""),
+          Array("", None, "", true, true, ""),
+          Array(null, null, null, true, true, ""),
+          Array("", Some("argvalue"), "", true, true, "'argvalue'")
+         )
+  }
+
+  @Test( dataProvider="formatArgumentTestData" )
+  def testFormatArgument( prefix: String, param: Any, suffix: String, spaceSeparated: Boolean, escape: Boolean, expectedReturnValue: String ) {
+    Assert.assertEquals(formatArgument(prefix, param, suffix, spaceSeparated, escape, "%s"),
+                        expectedReturnValue)
+  }
+
+  @Test
+  def testFormatArgumentCustomFormatString() {
+    Assert.assertEquals(formatArgument("", "argvalue", "", true, true, "%.3s"), "'arg'")
+  }
+
+  @DataProvider( name = "requiredTestData" )
+  def requiredDataProvider = {
+    Array(Array("", "argvalue", "", true, true, " 'argvalue' "),
+          Array("", "argvalue", "", true, false, " argvalue "),
+          Array("", "argvalue", "", false, true, " 'argvalue' "),
+          Array("", "argvalue", "", false, false, " argvalue "),
+          Array("-arg", "argvalue", "", true, true, " '-arg' 'argvalue' "),
+          Array("-arg", "argvalue", "", true, false, " -arg argvalue "),
+          Array("ARGNAME=", "ARGVALUE", "", false, true, " 'ARGNAME=ARGVALUE' "),
+          Array("ARGNAME=", "ARGVALUE", "", false, false, " ARGNAME=ARGVALUE "),
+          Array("-Xmx", "4", "G", true, true, " '-Xmx' '4' 'G' "),
+          Array("-Xmx", "4", "G", true, false, " -Xmx 4 G "),
+          Array("-Xmx", "4", "G", false, true, " '-Xmx4G' "),
+          Array("-Xmx", "4", "G", false, false, " -Xmx4G "),
+          Array("", "", "", true, true, " '' "),
+          Array("", "", "", true, false, "  "),
+          Array("", "", "", false, true, " '' "),
+          Array("", "", "", false, false, "  "),
+          Array("", null, "", true, true, "  "),
+          Array("", Nil, "", true, true, "  "),
+          Array("", None, "", true, true, "  ")
+         )
+  }
+
+  @Test( dataProvider="requiredTestData" )
+  def testRequired( prefix: String, param: Any, suffix: String, spaceSeparated: Boolean, escape: Boolean, expectedReturnValue: String ) {
+    Assert.assertEquals(required(prefix, param, suffix, spaceSeparated, escape),
+                        expectedReturnValue)
+  }
+
+  @DataProvider( name = "optionalTestData" )
+  def optionalDataProvider = {
+    Array(Array("-arg", "argvalue", "", true, true, " '-arg' 'argvalue' "),
+          Array("-arg", null, "", true, true, ""),
+          Array("-arg", Nil, "", true, true, ""),
+          Array("-arg", None, "", true, true, ""),
+          Array("-arg", "", "", true, true, " '-arg' ")
+         )
+  }
+
+  @Test( dataProvider="optionalTestData" )
+  def testOptional( prefix: String, param: Any, suffix: String, spaceSeparated: Boolean, escape: Boolean, expectedReturnValue: String ) {
+    Assert.assertEquals(optional(prefix, param, suffix, spaceSeparated, escape),
+                        expectedReturnValue)
+  }
+
+  @DataProvider( name = "conditionalTestData" )
+  def conditionalDataProvider = {
+    Array(Array(true, "-FLAG", true, " '-FLAG' "),
+          Array(true, "-FLAG", false, " -FLAG "),
+          Array(false, "-FLAG", true, ""),
+          Array(false, "-FLAG", false, ""),
+          Array(true, null, true, "  "),
+          Array(true, Nil, true, "  "),
+          Array(true, None, true, "  "),
+          Array(false, null, true, ""),
+          Array(false, Nil, true, ""),
+          Array(false, None, true, "")
+         )
+  }
+
+  @Test( dataProvider="conditionalTestData" )
+  def testConditional( condition: Boolean, param: Any, escape: Boolean, expectedReturnValue: String ) {
+    Assert.assertEquals(conditional(condition, param, escape),
+                        expectedReturnValue)
+  }
+
+  @DataProvider( name = "repeatTestData" )
+  def repeatDataProvider = {
+    Array(Array("", List("a", "bc", "d"), "", " ", true, true, " 'a' 'bc' 'd' "),
+          Array("", List("a", "bc", "d"), "", " ", true, false, " a bc d "),
+          Array("", List("a", "bc", "d"), "", "", true, true, " 'a''bc''d' "),
+          Array("", List("a", "bc", "d"), "", "", true, false, " abcd "),
+          Array("-f", List("file1", "file2", "file3"), "", " ", true, true, " '-f' 'file1' '-f' 'file2' '-f' 'file3' "),
+          Array("-f", List("file1", "file2", "file3"), "", " ", true, false, " -f file1 -f file2 -f file3 "),
+          Array("-f", List("file1", "file2", "file3"), "", " ", false, true, " '-ffile1' '-ffile2' '-ffile3' "),
+          Array("-f", List("file1", "file2", "file3"), "", " ", false, false, " -ffile1 -ffile2 -ffile3 "),
+          Array("-f", List("file1", "file2", "file3"), "", "", false, true, " '-ffile1''-ffile2''-ffile3' "),
+          Array("-f", List("file1", "file2", "file3"), "", "", false, false, " -ffile1-ffile2-ffile3 "),
+          Array("-f", List("file1", "file2", "file3"), "suffix", " ", true, true, " '-f' 'file1' 'suffix' '-f' 'file2' 'suffix' '-f' 'file3' 'suffix' "),
+          Array("-f", List("file1", "file2", "file3"), "suffix", " ", true, false, " -f file1 suffix -f file2 suffix -f file3 suffix "),
+          Array("-f", List("file1", "file2", "file3"), "suffix", " ", false, true, " '-ffile1suffix' '-ffile2suffix' '-ffile3suffix' "),
+          Array("-f", List("file1", "file2", "file3"), "suffix", " ", false, false, " -ffile1suffix -ffile2suffix -ffile3suffix "),
+          Array("-f", null, "", " ", true, true, ""),
+          Array("-f", Nil, "", " ", true, true, "")
+         )
+  }
+
+  @Test( dataProvider="repeatTestData" )
+  def testRepeat( prefix: String, params: Traversable[_], suffix: String, separator: String,
+                  spaceSeparated: Boolean, escape: Boolean, expectedReturnValue: String ) {
+    Assert.assertEquals(repeat(prefix, params, suffix, separator, spaceSeparated, escape),
+                        expectedReturnValue)
+  }
+
+  // Need to test None separately due to implicit conversion issues when using None in a TestNG data provider
+  @Test
+  def testRepeatNone() {
+    testRepeat("", None, "", " ", true, true, "")
+  }
+
+  @DataProvider( name = "repeatWithPrefixFormattingTestData" )
+  def repeatWithPrefixFormattingDataProvider = {
+    Array(Array("-f", List("file1", "file2", "file3"), "", " ", true, true, (prefix: String, value: Any) => "%s:tag%s".format(prefix, value),
+                " '-f:tagfile1' 'file1' '-f:tagfile2' 'file2' '-f:tagfile3' 'file3' "),
+          Array("-f", List("file1", "file2", "file3"), "", " ", true, false, (prefix: String, value: Any) => "%s:tag%s".format(prefix, value),
+                " -f:tagfile1 file1 -f:tagfile2 file2 -f:tagfile3 file3 "),
+          Array("", List("file1", "file2", "file3"), "", " ", true, true, (prefix: String, value: Any) => "-%s".format(value),
+                " '-file1' 'file1' '-file2' 'file2' '-file3' 'file3' "),
+          Array("-f", null, "", " ", true, true, (prefix: String, value: Any) => "%s:tag%s".format(prefix, value),
+                ""),
+          Array("-f", Nil, "", " ", true, true, (prefix: String, value: Any) => "%s:tag%s".format(prefix, value),
+                "")
+         )
+  }
+
+  @Test( dataProvider = "repeatWithPrefixFormattingTestData" )
+  def testRepeatWithPrefixFormatting( prefix: String, params: Traversable[_], suffix: String, separator: String,
+                                      spaceSeparated: Boolean, escape: Boolean, formatPrefix: (String, Any) => String,
+                                      expectedReturnValue: String ) {
+    Assert.assertEquals(repeat(prefix, params, suffix, separator, spaceSeparated, escape, "%s", formatPrefix),
+                        expectedReturnValue)
+  }
+}
\ No newline at end of file
diff --git a/public/scala/test/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala b/public/scala/test/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala
new file mode 100644
index 000000000..76585d207
--- /dev/null
+++ b/public/scala/test/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala
@@ -0,0 +1,57 @@
+package org.broadinstitute.sting.queue.util
+
+import org.testng.annotations.Test
+import org.testng.Assert
+import java.io.{InputStreamReader, BufferedReader}
+
+class ShellUtilsUnitTest {
+
+  @Test
+  def testEscapeShellArgumentOneCharSequences() {
+    // Test all ASCII characters except \0, \n, and \r, which we do not support escaping
+    for ( asciiCode <- 1 to 127 if asciiCode != 10 && asciiCode != 13  ) {
+      val originalString: String = "%c".format(asciiCode.toChar)
+      val quotedString: String = ShellUtils.escapeShellArgument(originalString)
+
+      val child : Process = new ProcessBuilder("/bin/sh", "-c", "printf \"%s\" " + quotedString).start()
+      val childReader : BufferedReader = new BufferedReader(new InputStreamReader(child.getInputStream))
+      val childOutputBuffer : StringBuilder = new StringBuilder
+
+      val childReaderThread : Thread = new Thread(new Runnable() {
+        def run() {
+          var line : String = childReader.readLine()
+
+          while ( line != null ) {
+            childOutputBuffer.append(line)
+            line = childReader.readLine()
+          }
+        }
+      })
+      childReaderThread.start()
+
+      val childReturnValue = child.waitFor()
+      childReaderThread.join()
+
+      childReader.close()
+      val childOutput = childOutputBuffer.toString()
+
+      if ( childReturnValue != 0 ) {
+        Assert.fail("With character ASCII %d, sh child process returned: %d".format(asciiCode, childReturnValue))
+      }
+      else if ( ! originalString.equals(childOutput) ) {
+        Assert.fail("With character ASCII %d, sh child process output \"%s\" instead of the expected \"%s\"".format(
+                    asciiCode, childOutput, originalString))
+      }
+    }
+  }
+
+  @Test(expectedExceptions = Array(classOf[IllegalArgumentException]))
+  def testEscapeShellArgumentNullString() {
+    ShellUtils.escapeShellArgument(null)
+  }
+
+  @Test
+  def testEscapeShellArgumentEmptyString() {
+    Assert.assertEquals(ShellUtils.escapeShellArgument(""), "''")
+  }
+}
\ No newline at end of file