Mercurial > repos > xuebing > sharplabtool
diff tools/gatk/count_covariates.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/gatk/count_covariates.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,431 @@ +<tool id="gatk_count_covariates" name="Count Covariates" version="0.0.1"> + <description>on BAM files</description> + <command interpreter="python">gatk_wrapper.py + --stdout "${output_log}" + -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" + -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index + -p 'java + -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" + -T "CountCovariates" + --num_threads 4 ##hard coded, for now + -et "NO_ET" ##ET no phone home + ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout + #if $reference_source.reference_source_selector != "history": + -R "${reference_source.ref_file.fields.path}" + #end if + --recal_file "${output_recal}" + ${standard_covs} + #if $covariates.value: + #for $cov in $covariates.value: + -cov "${cov}" + #end for + #end if + ' + + #set $snp_dataset_provided = False + #if str( $input_dbsnp_rod ) != "None": + -d "-D" "${input_dbsnp_rod}" "${input_dbsnp_rod.ext}" "dbsnp_rod" + #set $snp_dataset_provided = True + #end if + #set $rod_binding_names = dict() + #for $rod_binding in $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 + #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'snps': + #set $snp_dataset_provided = True + #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 + #end for + + ##start standard gatk options + #if $gatk_param_type.gatk_param_type_selector == "advanced": + #for $sample_metadata in $gatk_param_type.sample_metadata: + -p '--sample_metadata "${sample_metadata.sample_metadata_file}"' + #end for + #for $read_filter in $gatk_param_type.read_filter: + -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" + ###raise Exception( str( dir( $read_filter ) ) ) + #for $name, $param in $read_filter.read_filter_type.iteritems(): + #if $name not in [ "__current_case__", "read_filter_type_selector" ]: + --${name} "${param}" + #end if + #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}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals" + #end if + + -p '--BTI_merge_rule "${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} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"' + #end if + -p ' + --baq "${gatk_param_type.baq}" + --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}" + ${gatk_param_type.use_original_qualities} + --defaultBaseQualities "${gatk_param_type.default_base_qualities}" + --validation_strictness "${gatk_param_type.validation_strictness}" + --interval_merging "${gatk_param_type.interval_merging}" + ' + #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 + #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 + ##end standard gatk options + + ##start analysis specific options + #if $analysis_param_type.analysis_param_type_selector == "advanced": + -p ' + #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set": + --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}" + #end if + #if str( $analysis_param_type.default_platform ) != "default": + --default_platform "${analysis_param_type.default_platform}" + #end if + #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set": + --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}" + #end if + #if str( $analysis_param_type.force_platform ) != "default": + --force_platform "${analysis_param_type.force_platform}" + #end if + ${analysis_param_type.exception_if_no_tile} + #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set": + #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default": + --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}" + #end if + #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default": + --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}" + #end if + #end if + --window_size_nqs "${analysis_param_type.window_size_nqs}" + --homopolymer_nback "${analysis_param_type.homopolymer_nback}" + ' + #end if + #if not $snp_dataset_provided: + -p '--run_without_dbsnp_potentially_ruining_quality' + #end if + </command> + <inputs> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="input_bam" type="data" format="bam" label="BAM file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> + </param> + <param name="ref_file" type="select" label="Using reference genome"> + <options from_data_table="picard_indexes"> + <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> + </options> + </param> + </when> + <when value="history"> <!-- FIX ME!!!! --> + <param name="input_bam" type="data" format="bam" label="BAM file" /> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + <param name="standard_covs" type="boolean" truevalue="--standard_covs" falsevalue="" label="Use the standard set of covariates in addition to the ones selected" /> + <param name="covariates" type="select" multiple="True" display="checkboxes" label="Covariates to be used in the recalibration" > + <!-- might we want to load the available covariates from an external configuration file, since additional ones can be added to local installs? --> + <option value="ReadGroupCovariate" /> + <option value="QualityScoreCovariate" /> + <option value="CycleCovariate" /> + <option value="DinucCovariate" /> + <!-- covariates below were pull from source code, since the list option doesn't seem to work (when tried) --> + <option value="HomopolymerCovariate" /> + <option value="MappingQualityCovariate" /> + <option value="MinimumNQSCovariate" /> + <option value="PositionCovariate" /> + <option value="PrimerRoundCovariate" /> + <option value="TileCovariate" /> + </param> + <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" /> + <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="mask">Mask</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> + + <conditional name="gatk_param_type"> + <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic"> + <!-- Do nothing here --> + </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" /> + </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> + </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" /> + <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> + <option value="ALL_READS">ALL_READS</option> + <option value="BY_SAMPLE">BY_SAMPLE</option> + </param> + <when value="NONE"> + <!-- 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> + <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> + <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="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> + </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" /> + </when> + </conditional> + + <conditional name="analysis_param_type"> + <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> + <option value="basic" selected="True">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic"> + <!-- Do nothing here --> + </when> + <when value="advanced"> + <conditional name="default_read_group_type"> + <param name="default_read_group_type_selector" type="select" label="Set default Read Group"> + <option value="default" selected="True">Don't Set</option> + <option value="set">Set</option> + </param> + <when value="default"> + <!-- do nothing here --> + </when> + <when value="set"> + <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/> + </when> + </conditional> + <param name="default_platform" type="select" label="Set default Platform"> + <option value="default" selected="True">Don't Set</option> + <option value="illumina">illumina</option> + <option value="454">454</option> + <option value="solid">solid</option> + </param> + <conditional name="force_read_group_type"> + <param name="force_read_group_type_selector" type="select" label="Force Read Group"> + <option value="default" selected="True">Don't Force</option> + <option value="set">Force</option> + </param> + <when value="default"> + <!-- do nothing here --> + </when> + <when value="set"> + <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/> + </when> + </conditional> + <param name="force_platform" type="select" label="Force Platform"> + <option value="default" selected="True">Don't Force</option> + <option value="illumina">illumina</option> + <option value="454">454</option> + <option value="solid">solid</option> + </param> + <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found"/> + <conditional name="solid_options_type"> + <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options"> + <option value="default" selected="True">Don't Set</option> + <option value="set">Set</option> + </param> + <when value="default"> + <!-- do nothing here --> + </when> + <when value="set"> + <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted"> + <option value="default" selected="True">Don't set</option> + <option value="DO_NOTHING">DO_NOTHING</option> + <option value="SET_Q_ZERO">SET_Q_ZERO</option> + <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option> + <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option> + </param> + <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls"> + <option value="default" selected="True">Don't set</option> + <option value="THROW_EXCEPTION">THROW_EXCEPTION</option> + <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option> + <option value="PURGE_READ">PURGE_READ</option> + </param> + </when> + </conditional> + <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/> + <param name="homopolymer_nback" type="integer" value="7" label="number of previous bases to look at in HomopolymerCovariate" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="csv" name="output_recal" label="${tool.name} on ${on_string} (Covariate File)" /> + <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="phiX.fasta" ftype="fasta" /> + <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" /> + <param name="input_dbsnp_rod" /> + <param name="rod_bind_type_selector" value="snps" /> + <param name="rodToIntervalTrackName" /> + <param name="input_rod" value="gatk/fake_phiX_variant_locations.bed" ftype="bed" /> + <param name="standard_covs" value="True" /> + <param name="covariates" value="ReadGroupCovariate,HomopolymerCovariate,MinimumNQSCovariate,PositionCovariate" /> + <param name="gatk_param_type_selector" value="basic" /> + <param name="analysis_param_type_selector" value="basic" /> + <output name="output_recal" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" /> + <output name="output_log" file="gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains" compare="contains" /> + </test> + </tests> + <help> +.. class:: warningmark + +"This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation." +However, if you do not provide this file, the '--run_without_dbsnp_potentially_ruining_quality' flag will be automatically used, and the command will be allowed to run. + +**What it does** + + This walker is designed to work as the first pass in a two-pass processing step. It does a by-locus traversal + operating only at sites that are not in dbSNP. We assume that all reference mismatches we see are therefore errors + and indicative of poor base quality. This walker generates tables based on various user-specified covariates (such + as read group, reported quality score, cycle, and dinucleotide) Since there is a large amount of data one can then + calculate an empirical probability of error given the particular covariates seen at this site, where p(error) = num + mismatches / num observations The output file is a CSV list of (the several covariate values, num observations, num + mismatches, empirical quality score) The first non-comment line of the output file gives the name of the covariates + that were used for this calculation. Note: ReadGroupCovariate and QualityScoreCovariate are required covariates + and will be added for the user regardless of whether or not they were specified Note: This walker is designed to be + used in conjunction with TableRecalibrationWalker. + + +------ + +Please cite the website "http://addlink.here" as well as: + +Add citation here 2011. + +------ + +**Input formats** + +GenomeAnalysisTK: CountCovariates accepts an aligned BAM input file. + +------ + +**Outputs** + +The output is in CSV format, see http://addlink.here for more details. + +------- + +**Settings**:: + + + default_read_group If a read has no read group then default to the provided String. + default_platform If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid. + force_read_group If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group. + force_platform If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid. + window_size_nqs The window size used by MinimumNQSCovariate for its calculation + homopolymer_nback The number of previous bases to look at in HomopolymerCovariate + exception_if_no_tile If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1 + solid_recal_mode How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS) + solid_nocall_strategy Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ) + recal_file Filename for the input covariates table recalibration .csv file + out The output CSV file + recal_file Filename for the outputted covariates table recalibration file + standard_covs Use the standard set of covariates in addition to the ones listed using the -cov argument + run_without_dbsnp_potentially_ruining_quality If specified, allows the recalibrator to be used without a dbsnp rod. Very unsafe and for expert users only. + + </help> +</tool>