1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/ca2b29f0955e/ changeset: ca2b29f0955e user: dan date: 2011-10-31 19:27:48 summary: Update GATK command line options for gatk/indel_realigner.xml affected #: 1 file

diff -r 34ccc65185b34cb68f543fe041f3396e7897757c -r ca2b29f0955e00473e82ea2893bb954a4fecd21f tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -51,13 +51,16 @@ #end for ' #end for - #if str( $gatk_param_type.input_intervals ) != "None": - -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals" - #end if - #if str( $gatk_param_type.input_exclude_intervals ) != "None": - -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" - #end if + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ): + -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}" + #end for + + #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ): + -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}" + #end for + -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"' + -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"' #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE": -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -69,10 +72,16 @@ --defaultBaseQualities "${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} ' - #if str( $gatk_param_type.read_group_black_list ) != "None": - -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list" - #end if + #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_${rg_black_list_count}" + #else + -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"' + #end if + #end for #end if #if $reference_source.reference_source_selector == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"

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