comparison indel_realigner.xml @ 18:7533db8dfb5b draft

Update tool_dependencies to GATK v 2.3

17:f2b21dc45241

<tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.4">
  <description>- perform local realignment</description>
  <requirements>
      <requirement type="package" version="2.2">gatk</requirement>
      <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command interpreter="python">gatk2_wrapper.py
   --max_jvm_heap_fraction "1"
   --stdout "${output_log}"

   -p 'java 
    -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
    -T "IndelRealigner"
    -o "${output_bam}"
    \$GATK2_SITE_OPTIONS
    ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
    ##--num_threads 4 ##hard coded, for now
    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"

        ${gatk_param_type.use_original_qualities}
        --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
        --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.non_deterministic_random_seed}
        '
        #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"

          </conditional>
        </repeat>
        
        <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"/>
        
      </when>
    </conditional>
    
    <conditional name="analysis_param_type">

18:7533db8dfb5b

<tool id="gatk2_indel_realigner" name="Indel Realigner" version="0.0.5">
  <description>- perform local realignment</description>
  <requirements>
      <requirement type="package" version="2.3">gatk</requirement>
      <requirement type="package" version="0.1.18">samtools</requirement>
  </requirements>
  <command interpreter="python">gatk2_wrapper.py
   --max_jvm_heap_fraction "1"
   --stdout "${output_log}"

   -p 'java 
    -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
    -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
    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"

        ${gatk_param_type.use_original_qualities}
        --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
        --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 ):
            #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
                -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"

          </conditional>
        </repeat>
        
        <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>
    
    <conditional name="analysis_param_type">