diff variant_recalibrator.xml @ 18:7533db8dfb5b draft

Update tool_dependencies to GATK v 2.3

--- 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>