diff print_reads.xml @ 18:7533db8dfb5b draft

Update tool_dependencies to GATK v 2.3

--- 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>