comparison variant_eval.xml @ 1:c8752e31f496 draft

Uploaded

0:9ad15075b9fa

  <description></description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <command interpreter="python">gatk2_wrapper.py
   #from binascii import hexlify
   ##--max_jvm_heap_fraction "1"
   --stdout "${output_log}"
   #for $var_count, $variant in enumerate( $reference_source.variants ):
      -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}"
   #end for
   -p '
   @JAR_PATH@
    -T "VariantEval"
    --out "${output_report}"
    \$GATK2_SITE_OPTIONS

    @THREADS@

    ##-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}"
    #end if
   '
   

1:c8752e31f496

  <description></description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <command interpreter="python">
   #from binascii import hexlify

    gatk2_wrapper.py
   --stdout "${output_log}"
    #for $var_count, $variant in enumerate( $reference_source.variants ):
        -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}"
    #end for
    -p '
    @JAR_PATH@
    -T "VariantEval"
    --out "${output_report}"
    \$GATK2_SITE_OPTIONS

    @THREADS@

    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
   '