galaxy/tools/gatk/depth_of_coverage.xml

<tool id="gatk_depth_of_coverage" name="Depth of Coverage" version="0.0.2">
  <description>on BAM files</description>
  <requirements>
      <requirement type="package" version="1.4">gatk</requirement>
      <requirement type="package">samtools</requirement>
  </requirements>
  <macros>
    <import>gatk_macros.xml</import>
  </macros>
  <command interpreter="python">gatk_wrapper.py
   --max_jvm_heap_fraction "1"
   --stdout "${output_log}"
   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
       -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
       #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
           -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
       #end if
   #end for
   -p 'java 
    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
    -T "DepthOfCoverage"
    ##--num_threads 4 ##hard coded, for now
    
    -et "NO_ET" ##ET no phone home
    #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 ) == "":
            &amp;&amp; mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
            &amp;&amp; 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 ) == "" ):
            &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
            &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
        #end if
        #if str( $input_calculate_coverage_over_genes ) != "None":
            &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
            &amp;&amp; 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 ) == "":
            &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
            &amp;&amp; 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 ) == "":
            &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
            &amp;&amp; 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 ) == "" ):
            &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
            &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
        #end if
        #if str( $input_calculate_coverage_over_genes ) != "None":
            &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
            &amp;&amp; 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 ) == "":
            &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
            &amp;&amp; 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 ) == "":
            &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
            &amp;&amp; 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 ) == "" ):
            &amp;&amp; mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
            &amp;&amp; mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
        #end if
        #if str( $input_calculate_coverage_over_genes ) != "None":
            &amp;&amp; mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
            &amp;&amp; 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 ) == "":
            &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
            &amp;&amp; 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">
        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
            <param name="input_bam" type="data" format="bam" label="BAM file">
              <validator type="unspecified_build" />
              <validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
            </param>
        </repeat>
        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
          <options from_data_table="gatk_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!!!! -->
        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
            <param name="input_bam" type="data" format="bam" label="BAM file" />
        </repeat>
        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
      </when>
    </conditional>
    
    <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />
    
    <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &amp;lt;partitionType&amp;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 &amp;lt;summaryCoverageThreshold&amp;gt;">
        <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
    </repeat>
    
    <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;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 &amp;lt;maxBaseQuality&amp;gt;" />
        <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &amp;lt;minBaseQuality&amp;gt;" />
        <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &amp;lt;maxMappingQuality&amp;gt;" />
        <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality &amp;lt;minMappingQuality&amp;gt;" />
        <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &amp;lt;nBins&amp;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 &amp;lt;start&amp;gt;" />
        <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;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 &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Depth_of_Coverage&gt;`_.

To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.

If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.

------

**Inputs**

GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.


**Outputs**

The output is in various table formats.


Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ 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>
</tool>