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view depth_of_coverage.xml @ 9:dcf1482b628c draft
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| author | lz_hust |
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| date | Sat, 01 Jun 2019 07:09:27 -0400 |
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<tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1"> <description>on BAM files</description> <macros> <import>gatk2_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="version_command" /> <command interpreter="python">gatk2_wrapper.py ##--max_jvm_heap_fraction "1" --stdout "${output_log}" @BAM_INPUTS@ -p ' @JAR_PATH@ -T "DepthOfCoverage" \$GATK2_SITE_OPTIONS @THREADS@ #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" #end if #if str( $input_calculate_coverage_over_genes ) != "None": --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}" #end if #if str( $partition_type ) != "None": #for $pt in str( $partition_type ).split( ',' ): --partitionType "${pt}" #end for #end if --out "${output_per_locus_coverage}" #for $ct_group in $summary_coverage_threshold_group: --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}" #end for --outputFormat "${output_format}" ' #include source=$standard_gatk_options# ##start analysis specific options #if $analysis_param_type.analysis_param_type_selector == "advanced": -p ' ${analysis_param_type.ignore_deletion_sites} ${analysis_param_type.include_deletions} --maxBaseQuality "${analysis_param_type.max_base_quality}" --maxMappingQuality "${analysis_param_type.max_mapping_quality}" --minBaseQuality "${analysis_param_type.min_base_quality}" --minMappingQuality "${analysis_param_type.min_mapping_quality}" --nBins "${analysis_param_type.n_bins}" ${analysis_param_type.omit_depth_output_at_each_base} ${analysis_param_type.omit_interval_statistics} ${analysis_param_type.omit_locus_table} ${analysis_param_type.omit_per_sample_stats} ${analysis_param_type.print_base_counts} ${analysis_param_type.print_bin_endpoints_and_exit} --start "${analysis_param_type.start}" --stop "${analysis_param_type.stop}" ' #end if ##Move additional files to final location #if str( $partition_type ) != "None": #set $partition_types = str( $partition_type ).split( ',' ) #else: #set $partition_types = [ 'sample' ] #end if #if 'sample' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ): #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": && mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample} && mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample} #end if #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ): && mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample} && mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample} #end if #if str( $input_calculate_coverage_over_genes ) != "None": && mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample} && mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample} #end if #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": && mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample} && mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample} #end if #end if #if 'readgroup' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ): #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": && mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup} && mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup} #end if #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ): && mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup} && mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup} #end if #if str( $input_calculate_coverage_over_genes ) != "None": && mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup} && mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup} #end if #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup} && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup} #end if #end if #if 'library' in $partition_types and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.print_bin_endpoints_and_exit ) == "" ): #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": && mv ${output_per_locus_coverage}.library_summary ${output_summary_library} && mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library} #end if #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ): && mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library} && mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library} #end if #if str( $input_calculate_coverage_over_genes ) != "None": && mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library} && mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library} #end if #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": && mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library} && mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library} #end if #end if </command> <inputs> <conditional name="reference_source"> <expand macro="reference_source_selector_param" /> <when value="cached"> <expand macro="input_bams_cached" /> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk2_picard_indexes"> <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <!-- FIX ME!!!! --> <expand macro="input_bams_history" /> <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> </when> </conditional> <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &lt;calculateCoverageOverGenes&gt;" /> <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &lt;partitionType&gt;"> <option value="sample" selected="True">sample</option> <option value="readgroup">readgroup</option> <option value="library">library</option> </param> <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &lt;summaryCoverageThreshold&gt;"> <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to >= this number" /> </repeat> <param name="output_format" type="select" label="Output format" help="--outputFormat &lt;outputFormat&gt;" > <option value="csv">csv</option> <option value="table">table</option> <option value="rtable" selected="True">rtable</option> </param> <expand macro="gatk_param_type_conditional" /> <expand macro="analysis_type_conditional"> <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" /> <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" /> <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &lt;maxBaseQuality&gt;" /> <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &lt;minBaseQuality&gt;" /> <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &lt;maxMappingQuality&gt;" /> <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality &lt;minMappingQuality&gt;" /> <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &lt;nBins&gt;" /> <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" help="-omitBaseOutput,--omitDepthOutputAtEachBase" /> <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" /> <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" help="-omitLocusTable,--omitLocusTable" /> <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" /> <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" /> <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" /> <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &lt;start&gt;" /> <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &lt;stop&gt;" /> </expand> </inputs> <outputs> <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'sample' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'sample' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'sample' in partition_type or not partition_type</filter> <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'sample' in partition_type or not partition_type</filter> <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'sample' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'sample' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'readgroup' in partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'readgroup' in partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'readgroup' in partition_type</filter> <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'readgroup' in partition_type</filter> <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> <filter>'readgroup' in partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> <filter>'readgroup' in partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'library' in partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'library' in partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'library' in partition_type</filter> <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'library' in partition_type</filter> <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'library' in partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" > <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> <filter>'library' in partition_type</filter> <actions> <conditional name="output_format"> <when value="rtable"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> <when value="csv"> <action type="format"> <option type="from_param" name="output_format" /> </action> </when> </conditional> </actions> </data> <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" /> </outputs> <trackster_conf/> <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_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> <param name="input_calculate_coverage_over_genes" /> <param name="partition_type" value="sample" /> <param name="summary_coverage_threshold_group" value="0" /> <param name="output_format" value="rtable" /> <param name="gatk_param_type_selector" value="basic" /> <param name="analysis_param_type_selector" value="basic" /> <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" /> <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" /> <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" /> <output name="output_cumulative_coverage_counts_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_cumulative_coverage_counts_sample.tabular" /> <output name="output_cumulative_coverage_proportions_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_output_cumulative_coverage_proportions_sample.tabular" /> <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" /> </test> </tests> <help> **What it does** DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score. For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html>`_. To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. ------ **Inputs** GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files. **Outputs** The output is in various table formats. Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. ------- **Settings**:: calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. ignoreDeletionSites boolean false Ignore sites consisting only of deletions includeDeletions boolean false Include information on deletions maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. nBins int 499 Number of bins to use for granular binning omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. printBaseCounts boolean false Will add base counts to per-locus output. printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. start int 1 Starting (left endpoint) for granular binning stop int 500 Ending (right endpoint) for granular binning summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. @CITATION_SECTION@ </help> <expand macro="citations" /> </tool>