# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1356022915 21600
# Node ID 7533db8dfb5b1a91253d951a9b47b6ce72c92e72
# Parent  f2b21dc45241ebcc91c4fd4c214a2fdc5da01d80
Update tool_dependencies to GATK v 2.3

diff -r f2b21dc45241 -r 7533db8dfb5b README
--- a/README	Thu Nov 15 10:18:55 2012 -0600
+++ b/README	Thu Dec 20 11:01:55 2012 -0600
@@ -2,4 +2,18 @@
 copied into the tool-data directory.  The file tool_data_table_conf.xml must
 be edited to include references to these two new files.  
 
+GATK can be installed via tool_dependencies.   
+This will install GenomeAnalysisTKLite.jar from ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/ 
+and create a symbolic link from GenomeAnalysisTK.jar to GenomeAnalysisTKLite.jar
 
+If you have a full licensed copy of GenomeAnalysisTK.jar, change the GenomeAnalysisTK.jar symbolic link 
+in the installation directory to point to your licensed copy.
+
+Two environment variables: GATK2_SITE_OPTIONS and GATK2_THREAD_OPTIONS  are also set in the tool_dependencies env.sh file.
+You can alter the value of those variables for your site.
+$ cat tool_dependencies/gatk/2.2/*/gatk2/*/env.sh
+GATK2_PATH=/Users/jj/gxt/gxt/tool_dependencies/gatk/2.2/jimmy/gatk2/288cdae6bd9c; export GATK2_PATH
+GATK2_SITE_OPTIONS="--phone_home STANDARD"; export GATK2_SITE_OPTIONS
+GATK2_THREAD_OPTIONS="--num_threads 4 --num_cpu_threads_per_data_thread 3"; export GATK2_THREAD_OPTIONS
+
+
diff -r f2b21dc45241 -r 7533db8dfb5b base_recalibrator.xml
--- a/base_recalibrator.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/base_recalibrator.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.4">
+<tool id="gatk2_base_recalibrator" name="Base Recalibrator" version="0.0.5">
   <description>on BAM files</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
@@ -15,6 +15,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "BaseRecalibrator"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -90,6 +91,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -417,7 +419,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
-        
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
       </when>
     </conditional>
     
diff -r f2b21dc45241 -r 7533db8dfb5b depth_of_coverage.xml
--- a/depth_of_coverage.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/depth_of_coverage.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.4">
+<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.5">
   <description>on BAM files</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
@@ -17,6 +17,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "DepthOfCoverage"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##--num_threads 4 ##hard coded, for now
     
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
@@ -84,6 +85,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -437,6 +439,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b haplotype_caller.xml
--- a/haplotype_caller.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/haplotype_caller.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="0.0.4">
+<tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="0.0.5">
   <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
@@ -16,6 +16,7 @@
     -T "HaplotypeCaller"
     -o "${output_vcf}"
     ## \$GATK2_SITE_OPTIONS
+    ## \$GATK2_THREAD_OPTIONS
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
     ##--num_threads 4 ##not supported yet
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -70,6 +71,7 @@
         --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -417,6 +419,7 @@
         </repeat>
         
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b indel_realigner.xml
--- a/indel_realigner.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/indel_realigner.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.4">
+<tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.5">
   <description>- perform local realignment</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
@@ -16,6 +16,7 @@
     -T "IndelRealigner"
     -o "${output_bam}"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
     ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -82,6 +83,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -377,6 +379,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b print_reads.xml
--- a/print_reads.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/print_reads.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_print_reads" name="Print Reads" version="0.0.4">
+<tool id="gatk2_print_reads" name="Print Reads" version="0.0.5">
   <description>on BAM files</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
@@ -22,7 +22,9 @@
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
-    --BQSR "${input_recal}"
+    #if str($input_recal) != 'None':
+        --BQSR "${input_recal}"
+    #end if
     --disable_bam_indexing
    '
     ##start standard gatk options
@@ -70,6 +72,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -356,6 +359,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b realigner_target_creator.xml
--- a/realigner_target_creator.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/realigner_target_creator.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="0.0.4">
+<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="0.0.5">
   <description>for use in local realignment</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
@@ -16,6 +16,7 @@
     -T "RealignerTargetCreator"
     -o "${output_interval}"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
     ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -79,6 +80,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -363,6 +365,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b reduce_reads.xml
--- a/reduce_reads.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/reduce_reads.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_reduce_reads" name="Reduce Reads" version="0.0.4">
+<tool id="gatk2_reduce_reads" name="Reduce Reads" version="0.0.5">
   <description>in BAM files</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
@@ -16,6 +16,7 @@
     -T "ReduceReads"
     -o "${output_bam}"
     ## \$GATK2_SITE_OPTIONS
+    ## \$GATK2_THREAD_OPTIONS
     ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
     ##--num_threads 4 ##not supported yet
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -72,6 +73,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -363,6 +365,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/tool_dependencies.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="gatk" version="2.2">
+    <package name="gatk" version="2.3">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.2-8-g99996f2.tar.bz2</action>
+                <action type="download_by_url">ftp://ftp.broadinstitute.org/pub/gsa/GenomeAnalysisTK/GenomeAnalysisTKLite-2.3-4-gb8f1308.tar.bz2</action>
                 <action type="move_file">
                     <source>GenomeAnalysisTKLite.jar</source>
                     <destination>$INSTALL_DIR</destination>
@@ -15,7 +15,8 @@
                 </action>
                 <action type="set_environment">
                     <environment_variable name="GATK2_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">"--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD"</environment_variable>
+                    <environment_variable name="GATK2_SITE_OPTIONS" action="set_to">"--phone_home STANDARD"</environment_variable>
+                    <environment_variable name="GATK2_THREAD_OPTIONS" action="set_to">"--num_threads 4 --num_cpu_threads_per_data_thread 3"</environment_variable>
                 </action>
             </actions>
         </install>
diff -r f2b21dc45241 -r 7533db8dfb5b unified_genotyper.xml
--- a/unified_genotyper.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/unified_genotyper.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.4">
+<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.5">
   <description>SNP and indel caller</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
@@ -20,6 +20,7 @@
     --out "${output_vcf}"
     --metrics_file "${output_metrics}"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
@@ -85,6 +86,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -419,6 +421,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
@@ -458,7 +461,7 @@
         <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" help="--computeSLOD" />
         <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score &amp;lt;min_base_quality_score&amp;gt;" />
         <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to &lt; 0 or &gt; 1 (-deletions,--max_deletion_fraction &amp;lt;max_deletion_fraction&amp;gt;)" />
-        <param name="max_alternate_alleles" type="integer" value="5" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &amp;lt;max_alternate_alleles&amp;gt;" />
+        <param name="max_alternate_alleles" type="integer" value="6" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &amp;lt;max_alternate_alleles&amp;gt;" />
         <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &amp;lt;min_indel_count_for_genotyping&amp;gt;" />
         <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &amp;lt;indel_heterozygosity&amp;gt;)"/>
         <param name="indelGapContinuationPenalty" type="float" value="10.0" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty" />
diff -r f2b21dc45241 -r 7533db8dfb5b variant_annotator.xml
--- a/variant_annotator.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/variant_annotator.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.4">
+<tool id="gatk2_variant_annotator" name="Variant Annotator" version="0.0.5">
   <description></description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
@@ -19,6 +19,7 @@
     ##--list
     -T "VariantAnnotator"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -117,6 +118,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -444,6 +446,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b variant_apply_recalibration.xml
--- a/variant_apply_recalibration.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/variant_apply_recalibration.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.4">
+<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.5">
   <description></description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
    --max_jvm_heap_fraction "1"
@@ -13,6 +13,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "ApplyRecalibration"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
     #if $reference_source.reference_source_selector != "history":
@@ -68,6 +69,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -334,6 +336,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b variant_combine.xml
--- a/variant_combine.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/variant_combine.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_variant_combine" name="Combine Variants" version="0.0.4">
+<tool id="gatk2_variant_combine" name="Combine Variants" version="0.0.5">
   <description></description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
    --max_jvm_heap_fraction "1"
@@ -19,6 +19,7 @@
     -T "CombineVariants"
     --out "${output_variants}"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -74,6 +75,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -354,6 +356,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b variant_eval.xml
--- a/variant_eval.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/variant_eval.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_variant_eval" name="Eval Variants" version="0.0.4">
+<tool id="gatk2_variant_eval" name="Eval Variants" version="0.0.5">
   <description></description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
    #from binascii import hexlify
@@ -15,6 +15,7 @@
     -T "VariantEval"
     --out "${output_report}"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -82,6 +83,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -410,6 +412,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b variant_filtration.xml
--- a/variant_filtration.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/variant_filtration.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_variant_filtration" name="Variant Filtration" version="0.0.4">
+<tool id="gatk2_variant_filtration" name="Variant Filtration" version="0.0.5">
   <description>on VCF files</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
    #from binascii import hexlify
@@ -12,6 +12,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "VariantFiltration"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
     -o "${output_vcf}"
@@ -78,6 +79,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -363,6 +365,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b variant_recalibrator.xml
--- a/variant_recalibrator.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/variant_recalibrator.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="0.0.4">
+<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="0.0.5">
   <description></description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
    --max_jvm_heap_fraction "1"
@@ -13,6 +13,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "VariantRecalibrator"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file"##ET no phone home
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -86,6 +87,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -589,6 +591,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b variant_select.xml
--- a/variant_select.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/variant_select.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_variant_select" name="Select Variants" version="0.0.4">
+<tool id="gatk2_variant_select" name="Select Variants" version="0.0.5">
   <description>from VCF files</description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
    #from binascii import hexlify
@@ -12,6 +12,7 @@
     -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
     -T "SelectVariants"
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##--num_threads 4 ##hard coded, for now
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
     -o "${output_vcf}"
@@ -138,6 +139,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -408,6 +410,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>
diff -r f2b21dc45241 -r 7533db8dfb5b variants_validate.xml
--- a/variants_validate.xml	Thu Nov 15 10:18:55 2012 -0600
+++ b/variants_validate.xml	Thu Dec 20 11:01:55 2012 -0600
@@ -1,7 +1,7 @@
-<tool id="gatk2_validate_variants" name="Validate Variants" version="0.0.4">
+<tool id="gatk2_validate_variants" name="Validate Variants" version="0.0.5">
   <description></description>
   <requirements>
-      <requirement type="package" version="2.2">gatk</requirement>
+      <requirement type="package" version="2.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
    --max_jvm_heap_fraction "1"
@@ -12,6 +12,7 @@
     -T "ValidateVariants"
     
     \$GATK2_SITE_OPTIONS
+    \$GATK2_THREAD_OPTIONS
     ##-et "NO_ET" -K "\$GATK2_BASE/gatk2_key_file" ##ET no phone home
     ##--num_threads 4 ##hard coded, for now
     ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
@@ -71,6 +72,7 @@
         --validation_strictness "${gatk_param_type.validation_strictness}"
         --interval_merging "${gatk_param_type.interval_merging}"
         ${gatk_param_type.disable_experimental_low_memory_sharding}
+        ${gatk_param_type.fix_misencoded_quality_scores}
         ${gatk_param_type.non_deterministic_random_seed}
         '
         #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
@@ -334,6 +336,7 @@
         
         <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
         <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False"  help="-ndrs,--nonDeterministicRandomSeed"/>
+        <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False"  help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
         
       </when>
     </conditional>