[galaxy-commits] commit/galaxy-central: dan: Update generic GATK command line options.

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e494ac4c1e47/ changeset: e494ac4c1e47 user: dan date: 2011-10-21 19:48:24 summary: Update generic GATK command line options. affected #: 12 files (-1 bytes) --- a/tools/gatk/count_covariates.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/count_covariates.xml Fri Oct 21 13:48:24 2011 -0400 @@ -59,14 +59,16 @@ #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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -78,11 +80,18 @@ --defaultBaseQualities "${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 str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -202,7 +211,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -218,12 +227,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -240,7 +255,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -254,7 +269,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -267,19 +282,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/indel_realigner.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/indel_realigner.xml Fri Oct 21 13:48:24 2011 -0400 @@ -165,7 +165,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -181,12 +181,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -203,7 +209,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -217,7 +223,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -230,19 +236,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/realigner_target_creator.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/realigner_target_creator.xml Fri Oct 21 13:48:24 2011 -0400 @@ -47,12 +47,13 @@ #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 "${gatk_param_type.BTI_merge_rule}"' @@ -67,11 +68,18 @@ --defaultBaseQualities "${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" #end if @@ -151,7 +159,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -167,8 +175,12 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat><param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option> @@ -191,7 +203,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -205,7 +217,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -218,19 +230,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/table_recalibration.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/table_recalibration.xml Fri Oct 21 13:48:24 2011 -0400 @@ -35,29 +35,16 @@ #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 - #set $rod_binding_names = dict() - #for $rod_binding in $gatk_param_type.rod_bind: - #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': - #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name - #else - #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector - #end if - #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 - -d "-B:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" - #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ): - -p '--rodToIntervalTrackName "${rod_bind_name}"' - #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}"' - #if str( $gatk_param_type.input_dbsnp_rod ) != "None": - -d "-D" "${gatk_param_type.input_dbsnp_rod}" "${gatk_param_type.input_dbsnp_rod.ext}" "dbsnp_rod" - #end if + -p '--downsampling_type "${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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -69,11 +56,18 @@ --defaultBaseQualities "${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 str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -147,7 +141,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -163,35 +157,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> - <repeat name="rod_bind" title="Binding for reference-ordered data"> - <conditional name="rod_bind_type"> - <param name="rod_bind_type_selector" type="select" label="Binding Type"> - <option value="snps" selected="True">SNPs</option> - <option value="indels">INDELs</option> - <option value="custom">Custom</option> - </param> - <when value="snps"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="indels"> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - <when value="custom"> - <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> - <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" /> - <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" /> - </when> - </conditional> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /></repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> - <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" /> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -208,7 +185,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -222,7 +199,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -235,19 +212,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/unified_genotyper.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/unified_genotyper.xml Fri Oct 21 13:48:24 2011 -0400 @@ -56,12 +56,13 @@ #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 "${gatk_param_type.BTI_merge_rule}"' @@ -76,11 +77,18 @@ --defaultBaseQualities "${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" #end if @@ -194,7 +202,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -210,8 +218,12 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat><param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option> @@ -234,7 +246,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -248,7 +260,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -261,19 +273,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/variant_annotator.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_annotator.xml Fri Oct 21 13:48:24 2011 -0400 @@ -89,14 +89,16 @@ #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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -108,10 +110,16 @@ --defaultBaseQualities "${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 str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" @@ -252,28 +260,34 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> - </param> - <when value="ZeroMappingQualityRead"> - <!-- no extra options --> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> + <!-- no extra options --> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -281,55 +295,74 @@ <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> - <!-- no more options here --> - </when> + <!-- no more options here --> + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/variant_apply_recalibration.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_apply_recalibration.xml Fri Oct 21 13:48:24 2011 -0400 @@ -37,14 +37,16 @@ #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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -56,11 +58,18 @@ --defaultBaseQualities "${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 str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -118,28 +127,34 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> - </param> - <when value="ZeroMappingQualityRead"> - <!-- no extra options --> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> + <!-- no extra options --> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -147,55 +162,74 @@ <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> - <!-- no more options here --> - </when> + <!-- no more options here --> + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/variant_combine.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_combine.xml Fri Oct 21 13:48:24 2011 -0400 @@ -28,7 +28,6 @@ --rod_priority_list "${ ','.join( $priority_order ) }" ' - ##start standard gatk options #if $gatk_param_type.gatk_param_type_selector == "advanced": #for $sample_metadata in $gatk_param_type.sample_metadata: @@ -44,13 +43,16 @@ #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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -62,11 +64,18 @@ --defaultBaseQualities "${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" #end if @@ -138,7 +147,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -154,12 +163,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -176,7 +191,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -190,7 +205,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -203,19 +218,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/variant_eval.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_eval.xml Fri Oct 21 13:48:24 2011 -0400 @@ -56,13 +56,16 @@ #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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -74,11 +77,18 @@ --defaultBaseQualities "${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" #end if @@ -195,7 +205,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -211,12 +221,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -233,7 +249,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -247,7 +263,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -260,19 +276,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/variant_filtration.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_filtration.xml Fri Oct 21 13:48:24 2011 -0400 @@ -50,14 +50,16 @@ #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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -69,11 +71,18 @@ --defaultBaseQualities "${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 str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -152,7 +161,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -168,12 +177,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -190,7 +205,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -204,7 +219,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -217,19 +232,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/variant_recalibrator.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variant_recalibrator.xml Fri Oct 21 13:48:24 2011 -0400 @@ -58,14 +58,16 @@ #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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -77,11 +79,18 @@ --defaultBaseQualities "${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 str( $reference_source.reference_source_selector ) == "history": -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input" #end if @@ -382,28 +391,34 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> - <param name="read_filter_type_selector" type="select" label="Read Filter Type"> - <option value="MaxReadLength" selected="True">MaxReadLength</option> - <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> - </param> - <when value="ZeroMappingQualityRead"> - <!-- no extra options --> - </when> - <when value="MaxReadLength"> - <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> - </when> + <param name="read_filter_type_selector" type="select" label="Read Filter Type"> + <option value="MaxReadLength" selected="True">MaxReadLength</option> + <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option> + </param> + <when value="ZeroMappingQualityRead"> + <!-- no extra options --> + </when> + <when value="MaxReadLength"> + <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/> + </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -411,55 +426,74 @@ <option value="BY_SAMPLE">BY_SAMPLE</option></param><when value="NONE"> - <!-- no more options here --> - </when> + <!-- no more options here --> + </when><when value="ALL_READS"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when><when value="BY_SAMPLE"> - <conditional name="downsample_to_type"> - <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> - <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> - <option value="downsample_to_coverage">Downsample by Coverage</option> - </param> - <when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> - </when> - <when value="downsample_to_coverage"> - <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> - </when> - </conditional> - </when> + <conditional name="downsample_to_type"> + <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"> + <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option> + <option value="downsample_to_coverage">Downsample by Coverage</option> + </param> + <when value="downsample_to_fraction"> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/> + </when> + <when value="downsample_to_coverage"> + <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> + </when> + </conditional> + </when></conditional><param name="baq" type="select" label="Type of BAQ calculation to apply in the engine"><option value="OFF" selected="True">OFF</option><option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> --- a/tools/gatk/variants_validate.xml Fri Oct 21 10:32:57 2011 -0400 +++ b/tools/gatk/variants_validate.xml Fri Oct 21 13:48:24 2011 -0400 @@ -42,13 +42,16 @@ #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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' @@ -60,11 +63,18 @@ --defaultBaseQualities "${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" #end if @@ -120,7 +130,7 @@ </when><when value="advanced"><repeat name="sample_metadata" title="Sample Metadata"> - <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" /> + <param name="sample_metadata_file" type="data" format="txt" label="Sample file in JSON format" /></repeat><repeat name="read_filter" title="Read Filter"><conditional name="read_filter_type"> @@ -136,12 +146,18 @@ </when></conditional></repeat> - <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" /> - <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" /> + <repeat name="input_interval_repeat" title="Operate on Genomic intervals"> + <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals"> + <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list" label="Genomic intervals" /> + </repeat> + <param name="BTI_merge_rule" type="select" label="BTI merge rule"><option value="UNION" selected="True">UNION</option><option value="INTERSECTION">INTERSECTION</option></param> + <conditional name="downsampling_type"><param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type"><option value="NONE" selected="True">NONE</option> @@ -158,7 +174,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -172,7 +188,7 @@ <option value="downsample_to_coverage">Downsample by Coverage</option></param><when value="downsample_to_fraction"> - <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/> + <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1"/></when><when value="downsample_to_coverage"><param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/> @@ -185,19 +201,38 @@ <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option><option value="RECALCULATE">RECALCULATE</option></param> - <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/> + <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/><param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" /><param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/><param name="validation_strictness" type="select" label="How strict should we be with validation"><option value="STRICT" selected="True">STRICT</option><option value="LENIENT">LENIENT</option><option value="SILENT">SILENT</option> + <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...--></param><param name="interval_merging" type="select" label="Interval merging rule"><option value="ALL" selected="True">ALL</option><option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option></param> - <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" /> + + <repeat name="read_group_black_list_repeat" title="Read group black list"> + <conditional name="read_group_black_list_type"> + <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list"> + <option value="file" selected="True">Filters in file</option> + <option value="text">Specify filters as a string</option> + </param> + <when value="file"> + <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" /> + </when> + <when value="text"> + <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" /> + </when> + </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"/> + <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" /> + </when></conditional> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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