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1 <tool id="gatk_depth_of_coverage" name="Depth of Coverage" version="0.0.2">
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2 <description>on BAM files</description>
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3 <requirements>
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4 <requirement type="package" version="1.4">gatk</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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7 <macros>
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8 <import>gatk_macros.xml</import>
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9 </macros>
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10 <command interpreter="python">gatk_wrapper.py
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11 --max_jvm_heap_fraction "1"
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12 --stdout "${output_log}"
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13 #for $i, $input_bam in enumerate( $reference_source.input_bams ):
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14 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
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15 #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
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16 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
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17 #end if
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18 #end for
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19 -p 'java
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20 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
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21 -T "DepthOfCoverage"
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22 ##--num_threads 4 ##hard coded, for now
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23
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24 -et "NO_ET" ##ET no phone home
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25 #if $reference_source.reference_source_selector != "history":
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26 -R "${reference_source.ref_file.fields.path}"
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27 #end if
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28 #if str( $input_calculate_coverage_over_genes ) != "None":
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29 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}"
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30 #end if
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31 #if str( $partition_type ) != "None":
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32 #for $pt in str( $partition_type ).split( ',' ):
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33 --partitionType "${pt}"
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34 #end for
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35 #end if
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36 --out "${output_per_locus_coverage}"
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37
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38 #for $ct_group in $summary_coverage_threshold_group:
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39 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
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40 #end for
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41 --outputFormat "${output_format}"
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42 '
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43
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44 #include source=$standard_gatk_options#
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45 ##start analysis specific options
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46 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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47 -p '
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48 ${analysis_param_type.ignore_deletion_sites}
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49 ${analysis_param_type.include_deletions}
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50 --maxBaseQuality "${analysis_param_type.max_base_quality}"
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51 --maxMappingQuality "${analysis_param_type.max_mapping_quality}"
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52 --minBaseQuality "${analysis_param_type.min_base_quality}"
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53 --minMappingQuality "${analysis_param_type.min_mapping_quality}"
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54 --nBins "${analysis_param_type.n_bins}"
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55 ${analysis_param_type.omit_depth_output_at_each_base}
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56 ${analysis_param_type.omit_interval_statistics}
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57 ${analysis_param_type.omit_locus_table}
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58 ${analysis_param_type.omit_per_sample_stats}
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59 ${analysis_param_type.print_base_counts}
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60 ${analysis_param_type.print_bin_endpoints_and_exit}
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61 --start "${analysis_param_type.start}"
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62 --stop "${analysis_param_type.stop}"
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63 '
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64 #end if
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65 ##Move additional files to final location
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66 #if str( $partition_type ) != "None":
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67 #set $partition_types = str( $partition_type ).split( ',' )
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68 #else:
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69 #set $partition_types = [ 'sample' ]
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70 #end if
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71 #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 ) == "" ):
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72 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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73 && mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
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74 && mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample}
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75 #end if
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76 #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 ) == "" ):
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77 && mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
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78 && mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
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79 #end if
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80 #if str( $input_calculate_coverage_over_genes ) != "None":
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81 && mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
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82 && mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample}
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83 #end if
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84 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
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85 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
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86 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
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87 #end if
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88 #end if
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89
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90 #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 ) == "" ):
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91 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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92 && mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
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93 && mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
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94 #end if
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95 #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 ) == "" ):
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96 && mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
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97 && mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
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98 #end if
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99 #if str( $input_calculate_coverage_over_genes ) != "None":
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100 && mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
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101 && mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup}
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102 #end if
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103 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
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104 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
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105 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
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106 #end if
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107 #end if
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108
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109 #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 ) == "" ):
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110 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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111 && mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
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112 && mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
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113 #end if
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114 #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 ) == "" ):
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115 && mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
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116 && mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
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117 #end if
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118 #if str( $input_calculate_coverage_over_genes ) != "None":
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119 && mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
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120 && mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library}
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121 #end if
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122 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
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123 && mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
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124 && mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
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125 #end if
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126 #end if
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127
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128
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129 </command>
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130 <inputs>
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131 <conditional name="reference_source">
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132 <expand macro="reference_source_selector_param" />
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133 <when value="cached">
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134 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;">
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135 <param name="input_bam" type="data" format="bam" label="BAM file">
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136 <validator type="unspecified_build" />
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137 <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 -->
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138 </param>
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139 </repeat>
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140 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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141 <options from_data_table="gatk_picard_indexes">
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142 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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143 </options>
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144 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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145 </param>
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146 </when>
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147 <when value="history"> <!-- FIX ME!!!! -->
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148 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;">
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149 <param name="input_bam" type="data" format="bam" label="BAM file" />
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150 </repeat>
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151 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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152 </when>
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153 </conditional>
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154
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155 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &lt;calculateCoverageOverGenes&gt;" />
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156
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157 <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &lt;partitionType&gt;">
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158 <option value="sample" selected="True">sample</option>
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159 <option value="readgroup">readgroup</option>
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160 <option value="library">library</option>
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161 </param>
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162
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163 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &lt;summaryCoverageThreshold&gt;">
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164 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to >= this number" />
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165 </repeat>
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166
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167 <param name="output_format" type="select" label="Output format" help="--outputFormat &lt;outputFormat&gt;" >
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168 <option value="csv">csv</option>
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169 <option value="table">table</option>
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170 <option value="rtable" selected="True">rtable</option>
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171 </param>
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172
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173 <expand macro="gatk_param_type_conditional" />
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174
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175 <expand macro="analysis_type_conditional">
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176 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
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177 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
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178 <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &lt;maxBaseQuality&gt;" />
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179 <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &lt;minBaseQuality&gt;" />
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180 <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &lt;maxMappingQuality&gt;" />
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181 <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;" />
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182 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &lt;nBins&gt;" />
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183 <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" />
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184 <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" />
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185 <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" />
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186 <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" />
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187 <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" />
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188 <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
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189 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &lt;start&gt;" />
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190 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &lt;stop&gt;" />
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191 </expand>
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192 </inputs>
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193 <outputs>
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194 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
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195 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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196 <actions>
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197 <conditional name="output_format">
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198 <when value="rtable">
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199 <action type="format">
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200 <option type="from_param" name="output_format" />
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201 </action>
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202 </when>
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203 <when value="csv">
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204 <action type="format">
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205 <option type="from_param" name="output_format" />
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206 </action>
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207 </when>
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208 </conditional>
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209 </actions>
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210 </data>
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211 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" >
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212 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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213 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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214 <filter>'sample' in partition_type or not partition_type</filter>
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215 <actions>
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216 <conditional name="output_format">
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217 <when value="rtable">
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218 <action type="format">
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219 <option type="from_param" name="output_format" />
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220 </action>
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221 </when>
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222 <when value="csv">
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223 <action type="format">
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224 <option type="from_param" name="output_format" />
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225 </action>
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226 </when>
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227 </conditional>
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228 </actions>
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229 </data>
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230 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" >
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231 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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232 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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233 <filter>'sample' in partition_type or not partition_type</filter>
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234 <actions>
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235 <conditional name="output_format">
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236 <when value="rtable">
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237 <action type="format">
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238 <option type="from_param" name="output_format" />
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239 </action>
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240 </when>
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241 <when value="csv">
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242 <action type="format">
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243 <option type="from_param" name="output_format" />
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244 </action>
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245 </when>
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246 </conditional>
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247 </actions>
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248 </data>
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249 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" >
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250 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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251 <filter>'sample' in partition_type or not partition_type</filter>
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252 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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253 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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254 <actions>
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255 <conditional name="output_format">
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256 <when value="rtable">
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257 <action type="format">
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258 <option type="from_param" name="output_format" />
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259 </action>
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260 </when>
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261 <when value="csv">
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262 <action type="format">
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263 <option type="from_param" name="output_format" />
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264 </action>
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265 </when>
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266 </conditional>
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267 </actions>
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268 </data>
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269 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" >
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270 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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271 <filter>'sample' in partition_type or not partition_type</filter>
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272 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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273 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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274 <actions>
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275 <conditional name="output_format">
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276 <when value="rtable">
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277 <action type="format">
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278 <option type="from_param" name="output_format" />
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279 </action>
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280 </when>
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281 <when value="csv">
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282 <action type="format">
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283 <option type="from_param" name="output_format" />
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284 </action>
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285 </when>
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286 </conditional>
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287 </actions>
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288 </data>
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289 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" >
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290 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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291 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
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292 <actions>
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293 <conditional name="output_format">
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294 <when value="rtable">
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295 <action type="format">
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296 <option type="from_param" name="output_format" />
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297 </action>
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298 </when>
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299 <when value="csv">
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300 <action type="format">
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301 <option type="from_param" name="output_format" />
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302 </action>
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303 </when>
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304 </conditional>
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305 </actions>
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306 </data>
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307 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" >
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308 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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309 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
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310 <actions>
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311 <conditional name="output_format">
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312 <when value="rtable">
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313 <action type="format">
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314 <option type="from_param" name="output_format" />
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315 </action>
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316 </when>
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317 <when value="csv">
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318 <action type="format">
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319 <option type="from_param" name="output_format" />
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320 </action>
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321 </when>
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322 </conditional>
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323 </actions>
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324 </data>
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325 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" >
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326 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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327 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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328 <filter>'sample' in partition_type or not partition_type</filter>
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329 <actions>
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330 <conditional name="output_format">
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331 <when value="rtable">
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332 <action type="format">
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333 <option type="from_param" name="output_format" />
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334 </action>
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335 </when>
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336 <when value="csv">
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337 <action type="format">
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338 <option type="from_param" name="output_format" />
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339 </action>
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340 </when>
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341 </conditional>
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342 </actions>
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343 </data>
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344 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" >
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345 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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346 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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347 <filter>'sample' in partition_type or not partition_type</filter>
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348 <actions>
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349 <conditional name="output_format">
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350 <when value="rtable">
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351 <action type="format">
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352 <option type="from_param" name="output_format" />
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353 </action>
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354 </when>
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355 <when value="csv">
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356 <action type="format">
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357 <option type="from_param" name="output_format" />
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358 </action>
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359 </when>
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360 </conditional>
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361 </actions>
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362 </data>
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363
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364 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
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365 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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366 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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367 <filter>'readgroup' in partition_type</filter>
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368 <actions>
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369 <conditional name="output_format">
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370 <when value="rtable">
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371 <action type="format">
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372 <option type="from_param" name="output_format" />
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373 </action>
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374 </when>
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375 <when value="csv">
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376 <action type="format">
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377 <option type="from_param" name="output_format" />
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378 </action>
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379 </when>
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380 </conditional>
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381 </actions>
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382 </data>
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383 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" >
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384 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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385 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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386 <filter>'readgroup' in partition_type</filter>
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387 <actions>
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388 <conditional name="output_format">
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389 <when value="rtable">
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390 <action type="format">
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391 <option type="from_param" name="output_format" />
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392 </action>
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393 </when>
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394 <when value="csv">
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395 <action type="format">
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396 <option type="from_param" name="output_format" />
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397 </action>
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398 </when>
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399 </conditional>
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400 </actions>
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401 </data>
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402 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" >
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403 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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404 <filter>'readgroup' in partition_type</filter>
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405 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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|
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406 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
|
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407 <actions>
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408 <conditional name="output_format">
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409 <when value="rtable">
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410 <action type="format">
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411 <option type="from_param" name="output_format" />
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412 </action>
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413 </when>
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414 <when value="csv">
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415 <action type="format">
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|
416 <option type="from_param" name="output_format" />
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417 </action>
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418 </when>
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419 </conditional>
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420 </actions>
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421 </data>
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422 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" >
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423 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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|
|
424 <filter>'readgroup' in partition_type</filter>
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425 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
|
|
|
426 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
|
|
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427 <actions>
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428 <conditional name="output_format">
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429 <when value="rtable">
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430 <action type="format">
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|
431 <option type="from_param" name="output_format" />
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|
432 </action>
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433 </when>
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434 <when value="csv">
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435 <action type="format">
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|
436 <option type="from_param" name="output_format" />
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437 </action>
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438 </when>
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439 </conditional>
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440 </actions>
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441 </data>
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|
442 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" >
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|
443 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
444 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
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|
|
445 <actions>
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446 <conditional name="output_format">
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447 <when value="rtable">
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|
448 <action type="format">
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|
449 <option type="from_param" name="output_format" />
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450 </action>
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|
451 </when>
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|
452 <when value="csv">
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|
453 <action type="format">
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|
454 <option type="from_param" name="output_format" />
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|
455 </action>
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456 </when>
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|
457 </conditional>
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|
458 </actions>
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|
459 </data>
|
|
|
460 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" >
|
|
|
461 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
462 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
|
|
|
463 <actions>
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|
464 <conditional name="output_format">
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|
465 <when value="rtable">
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|
|
466 <action type="format">
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|
467 <option type="from_param" name="output_format" />
|
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|
468 </action>
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|
|
469 </when>
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|
470 <when value="csv">
|
|
|
471 <action type="format">
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|
472 <option type="from_param" name="output_format" />
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|
473 </action>
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|
474 </when>
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|
475 </conditional>
|
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476 </actions>
|
|
|
477 </data>
|
|
|
478 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" >
|
|
|
479 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
480 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
|
|
|
481 <filter>'readgroup' in partition_type</filter>
|
|
|
482 <actions>
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|
|
483 <conditional name="output_format">
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|
484 <when value="rtable">
|
|
|
485 <action type="format">
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|
486 <option type="from_param" name="output_format" />
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|
487 </action>
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488 </when>
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|
489 <when value="csv">
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|
490 <action type="format">
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|
491 <option type="from_param" name="output_format" />
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|
492 </action>
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|
493 </when>
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494 </conditional>
|
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|
495 </actions>
|
|
|
496 </data>
|
|
|
497 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" >
|
|
|
498 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
499 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
|
|
|
500 <filter>'readgroup' in partition_type</filter>
|
|
|
501 <actions>
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|
502 <conditional name="output_format">
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|
503 <when value="rtable">
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|
504 <action type="format">
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|
505 <option type="from_param" name="output_format" />
|
|
|
506 </action>
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|
507 </when>
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508 <when value="csv">
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|
509 <action type="format">
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|
510 <option type="from_param" name="output_format" />
|
|
|
511 </action>
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512 </when>
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513 </conditional>
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|
514 </actions>
|
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|
515 </data>
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|
|
516
|
|
|
517 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
|
|
|
518 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
|
|
|
519 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
520 <filter>'library' in partition_type</filter>
|
|
|
521 <actions>
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|
522 <conditional name="output_format">
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|
523 <when value="rtable">
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|
524 <action type="format">
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|
525 <option type="from_param" name="output_format" />
|
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|
526 </action>
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|
527 </when>
|
|
|
528 <when value="csv">
|
|
|
529 <action type="format">
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|
|
530 <option type="from_param" name="output_format" />
|
|
|
531 </action>
|
|
|
532 </when>
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|
|
533 </conditional>
|
|
|
534 </actions>
|
|
|
535 </data>
|
|
|
536 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" >
|
|
|
537 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
|
|
|
538 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
539 <filter>'library' in partition_type</filter>
|
|
|
540 <actions>
|
|
|
541 <conditional name="output_format">
|
|
|
542 <when value="rtable">
|
|
|
543 <action type="format">
|
|
|
544 <option type="from_param" name="output_format" />
|
|
|
545 </action>
|
|
|
546 </when>
|
|
|
547 <when value="csv">
|
|
|
548 <action type="format">
|
|
|
549 <option type="from_param" name="output_format" />
|
|
|
550 </action>
|
|
|
551 </when>
|
|
|
552 </conditional>
|
|
|
553 </actions>
|
|
|
554 </data>
|
|
|
555 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" >
|
|
|
556 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
557 <filter>'library' in partition_type</filter>
|
|
|
558 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
|
|
|
559 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
|
|
|
560 <actions>
|
|
|
561 <conditional name="output_format">
|
|
|
562 <when value="rtable">
|
|
|
563 <action type="format">
|
|
|
564 <option type="from_param" name="output_format" />
|
|
|
565 </action>
|
|
|
566 </when>
|
|
|
567 <when value="csv">
|
|
|
568 <action type="format">
|
|
|
569 <option type="from_param" name="output_format" />
|
|
|
570 </action>
|
|
|
571 </when>
|
|
|
572 </conditional>
|
|
|
573 </actions>
|
|
|
574 </data>
|
|
|
575 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" >
|
|
|
576 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
577 <filter>'library' in partition_type</filter>
|
|
|
578 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
|
|
|
579 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
|
|
|
580 <actions>
|
|
|
581 <conditional name="output_format">
|
|
|
582 <when value="rtable">
|
|
|
583 <action type="format">
|
|
|
584 <option type="from_param" name="output_format" />
|
|
|
585 </action>
|
|
|
586 </when>
|
|
|
587 <when value="csv">
|
|
|
588 <action type="format">
|
|
|
589 <option type="from_param" name="output_format" />
|
|
|
590 </action>
|
|
|
591 </when>
|
|
|
592 </conditional>
|
|
|
593 </actions>
|
|
|
594 </data>
|
|
|
595 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" >
|
|
|
596 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
597 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
|
|
|
598 <actions>
|
|
|
599 <conditional name="output_format">
|
|
|
600 <when value="rtable">
|
|
|
601 <action type="format">
|
|
|
602 <option type="from_param" name="output_format" />
|
|
|
603 </action>
|
|
|
604 </when>
|
|
|
605 <when value="csv">
|
|
|
606 <action type="format">
|
|
|
607 <option type="from_param" name="output_format" />
|
|
|
608 </action>
|
|
|
609 </when>
|
|
|
610 </conditional>
|
|
|
611 </actions>
|
|
|
612 </data>
|
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613 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" >
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614 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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615 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
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616 <actions>
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617 <conditional name="output_format">
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618 <when value="rtable">
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619 <action type="format">
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620 <option type="from_param" name="output_format" />
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621 </action>
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622 </when>
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623 <when value="csv">
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624 <action type="format">
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625 <option type="from_param" name="output_format" />
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626 </action>
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627 </when>
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628 </conditional>
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629 </actions>
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630 </data>
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631 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" >
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632 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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633 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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634 <filter>'library' in partition_type</filter>
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635 <actions>
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636 <conditional name="output_format">
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637 <when value="rtable">
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638 <action type="format">
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639 <option type="from_param" name="output_format" />
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640 </action>
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641 </when>
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642 <when value="csv">
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643 <action type="format">
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644 <option type="from_param" name="output_format" />
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645 </action>
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646 </when>
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647 </conditional>
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648 </actions>
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649 </data>
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650 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" >
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651 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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652 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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653 <filter>'library' in partition_type</filter>
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654 <actions>
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655 <conditional name="output_format">
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656 <when value="rtable">
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657 <action type="format">
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658 <option type="from_param" name="output_format" />
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659 </action>
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660 </when>
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661 <when value="csv">
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662 <action type="format">
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663 <option type="from_param" name="output_format" />
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664 </action>
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665 </when>
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666 </conditional>
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667 </actions>
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668 </data>
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669
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670 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
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671 </outputs>
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672 <trackster_conf/>
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673 <tests>
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674 <test>
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675 <param name="reference_source_selector" value="history" />
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676 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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677 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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678 <param name="input_calculate_coverage_over_genes" />
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679 <param name="partition_type" value="sample" />
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680 <param name="summary_coverage_threshold_group" value="0" />
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|
681 <param name="output_format" value="rtable" />
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|
|
682 <param name="gatk_param_type_selector" value="basic" />
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|
683 <param name="analysis_param_type_selector" value="basic" />
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684 <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" />
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685 <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" />
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686 <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" />
|
|
|
687 <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" />
|
|
|
688 <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" />
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|
|
689 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" />
|
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690 </test>
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691 </tests>
|
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692 <help>
|
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|
693 **What it does**
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694
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695 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.
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696
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697 For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Depth_of_Coverage>`_.
|
|
|
698
|
|
|
699 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_.
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700
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|
|
701 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
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|
702
|
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|
703 ------
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704
|
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|
705 **Inputs**
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706
|
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|
707 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.
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|
|
708
|
|
|
709
|
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710 **Outputs**
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711
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712 The output is in various table formats.
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|
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713
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|
|
714
|
|
|
715 Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
|
|
|
716
|
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|
717 -------
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|
|
718
|
|
|
719 **Settings**::
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|
|
720
|
|
|
721 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
|
|
|
722 ignoreDeletionSites boolean false Ignore sites consisting only of deletions
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|
|
723 includeDeletions boolean false Include information on deletions
|
|
|
724 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
|
|
|
725 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
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|
|
726 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
|
|
|
727 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
|
|
|
728 nBins int 499 Number of bins to use for granular binning
|
|
|
729 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
|
|
|
730 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
|
|
|
731 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
|
|
|
732 omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
|
|
|
733 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
|
|
|
734 partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
|
|
|
735 printBaseCounts boolean false Will add base counts to per-locus output.
|
|
|
736 printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
|
|
|
737 start int 1 Starting (left endpoint) for granular binning
|
|
|
738 stop int 500 Ending (right endpoint) for granular binning
|
|
|
739 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
|
|
|
740
|
|
|
741 @CITATION_SECTION@
|
|
|
742 </help>
|
|
|
743 </tool>
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