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4
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1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0">
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0
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2 <description>on BAM files</description>
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3 <expand macro="requirements" />
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4 <macros>
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5 <import>gatk2_macros.xml</import>
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6 </macros>
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7 <command interpreter="python">gatk2_wrapper.py
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8 ##--max_jvm_heap_fraction "1"
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9 --stdout "${output_log}"
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10 #for $i, $input_bam in enumerate( $reference_source.input_bams ):
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11 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
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12 #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
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13 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
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14 #end if
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15 #end for
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16 -p '
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17 @JAR_PATH@
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18 -T "DepthOfCoverage"
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19 \$GATK2_SITE_OPTIONS
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20
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21 @THREADS@
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22
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23 #if $reference_source.reference_source_selector != "history":
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24 -R "${reference_source.ref_file.fields.path}"
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25 #end if
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26 #if str( $input_calculate_coverage_over_genes ) != "None":
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27 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}"
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28 #end if
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29 #if str( $partition_type ) != "None":
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30 #for $pt in str( $partition_type ).split( ',' ):
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31 --partitionType "${pt}"
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32 #end for
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33 #end if
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34 --out "${output_per_locus_coverage}"
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35
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36 #for $ct_group in $summary_coverage_threshold_group:
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37 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
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38 #end for
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39 --outputFormat "${output_format}"
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40 '
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41
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42 #include source=$standard_gatk_options#
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43 ##start analysis specific options
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44 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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45 -p '
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46 ${analysis_param_type.ignore_deletion_sites}
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47 ${analysis_param_type.include_deletions}
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48 --maxBaseQuality "${analysis_param_type.max_base_quality}"
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49 --maxMappingQuality "${analysis_param_type.max_mapping_quality}"
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50 --minBaseQuality "${analysis_param_type.min_base_quality}"
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51 --minMappingQuality "${analysis_param_type.min_mapping_quality}"
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52 --nBins "${analysis_param_type.n_bins}"
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53 ${analysis_param_type.omit_depth_output_at_each_base}
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54 ${analysis_param_type.omit_interval_statistics}
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55 ${analysis_param_type.omit_locus_table}
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56 ${analysis_param_type.omit_per_sample_stats}
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57 ${analysis_param_type.print_base_counts}
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58 ${analysis_param_type.print_bin_endpoints_and_exit}
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59 --start "${analysis_param_type.start}"
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60 --stop "${analysis_param_type.stop}"
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61 '
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62 #end if
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63 ##Move additional files to final location
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64 #if str( $partition_type ) != "None":
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65 #set $partition_types = str( $partition_type ).split( ',' )
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66 #else:
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67 #set $partition_types = [ 'sample' ]
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68 #end if
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69 #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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70 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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71 && mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
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72 && mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample}
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73 #end if
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74 #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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75 && mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
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76 && mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
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77 #end if
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78 #if str( $input_calculate_coverage_over_genes ) != "None":
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79 && mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
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80 && mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample}
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81 #end if
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82 #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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83 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
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84 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
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85 #end if
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86 #end if
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87
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88 #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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89 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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90 && mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
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91 && mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
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92 #end if
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93 #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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94 && mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
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95 && mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
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96 #end if
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97 #if str( $input_calculate_coverage_over_genes ) != "None":
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98 && mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
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99 && mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup}
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100 #end if
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101 #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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102 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
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103 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
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104 #end if
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105 #end if
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106
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107 #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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108 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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109 && mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
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110 && mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
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111 #end if
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112 #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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113 && mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
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114 && mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
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115 #end if
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116 #if str( $input_calculate_coverage_over_genes ) != "None":
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117 && mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
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118 && mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library}
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119 #end if
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120 #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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121 && mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
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122 && mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
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123 #end if
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124 #end if
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125
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126
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127 </command>
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128 <inputs>
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129 <conditional name="reference_source">
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130 <expand macro="reference_source_selector_param" />
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131 <when value="cached">
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132 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;">
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133 <param name="input_bam" type="data" format="bam" label="BAM file">
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134 <validator type="unspecified_build" />
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135 <validator type="dataset_metadata_in_data_table" table_name="gatk2_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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136 </param>
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137 </repeat>
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138 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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139 <options from_data_table="gatk2_picard_indexes">
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140 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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141 </options>
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142 <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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143 </param>
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144 </when>
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145 <when value="history"> <!-- FIX ME!!!! -->
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146 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;">
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147 <param name="input_bam" type="data" format="bam" label="BAM file" />
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148 </repeat>
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149 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
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150 </when>
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151 </conditional>
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152
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153 <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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154
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155 <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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156 <option value="sample" selected="True">sample</option>
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157 <option value="readgroup">readgroup</option>
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158 <option value="library">library</option>
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159 </param>
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160
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161 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &lt;summaryCoverageThreshold&gt;">
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162 <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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163 </repeat>
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164
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165 <param name="output_format" type="select" label="Output format" help="--outputFormat &lt;outputFormat&gt;" >
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166 <option value="csv">csv</option>
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167 <option value="table">table</option>
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168 <option value="rtable" selected="True">rtable</option>
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169 </param>
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170
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171 <expand macro="gatk_param_type_conditional" />
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172
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173 <expand macro="analysis_type_conditional">
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174 <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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175 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
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176 <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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177 <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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178 <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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179 <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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180 <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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181 <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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182 <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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183 <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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184 <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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185 <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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186 <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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187 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &lt;start&gt;" />
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188 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &lt;stop&gt;" />
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189 </expand>
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190 </inputs>
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191 <outputs>
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192 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
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193 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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194 <actions>
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195 <conditional name="output_format">
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196 <when value="rtable">
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197 <action type="format">
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198 <option type="from_param" name="output_format" />
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199 </action>
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200 </when>
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201 <when value="csv">
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202 <action type="format">
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203 <option type="from_param" name="output_format" />
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204 </action>
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205 </when>
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206 </conditional>
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207 </actions>
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208 </data>
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209 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" >
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210 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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211 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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212 <filter>'sample' in partition_type or not partition_type</filter>
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213 <actions>
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214 <conditional name="output_format">
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215 <when value="rtable">
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216 <action type="format">
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217 <option type="from_param" name="output_format" />
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218 </action>
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219 </when>
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220 <when value="csv">
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221 <action type="format">
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222 <option type="from_param" name="output_format" />
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223 </action>
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224 </when>
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225 </conditional>
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226 </actions>
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227 </data>
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228 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" >
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229 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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230 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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231 <filter>'sample' in partition_type or not partition_type</filter>
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232 <actions>
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233 <conditional name="output_format">
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234 <when value="rtable">
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235 <action type="format">
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236 <option type="from_param" name="output_format" />
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237 </action>
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238 </when>
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239 <when value="csv">
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240 <action type="format">
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241 <option type="from_param" name="output_format" />
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242 </action>
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243 </when>
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244 </conditional>
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245 </actions>
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246 </data>
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247 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" >
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248 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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249 <filter>'sample' in partition_type or not partition_type</filter>
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250 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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251 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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252 <actions>
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253 <conditional name="output_format">
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254 <when value="rtable">
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255 <action type="format">
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256 <option type="from_param" name="output_format" />
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257 </action>
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258 </when>
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259 <when value="csv">
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260 <action type="format">
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261 <option type="from_param" name="output_format" />
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262 </action>
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263 </when>
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264 </conditional>
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265 </actions>
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266 </data>
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267 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" >
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268 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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269 <filter>'sample' in partition_type or not partition_type</filter>
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270 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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271 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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272 <actions>
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273 <conditional name="output_format">
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274 <when value="rtable">
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275 <action type="format">
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276 <option type="from_param" name="output_format" />
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277 </action>
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278 </when>
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279 <when value="csv">
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280 <action type="format">
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281 <option type="from_param" name="output_format" />
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282 </action>
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283 </when>
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284 </conditional>
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285 </actions>
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286 </data>
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287 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" >
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288 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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289 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
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290 <actions>
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291 <conditional name="output_format">
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292 <when value="rtable">
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293 <action type="format">
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294 <option type="from_param" name="output_format" />
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295 </action>
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296 </when>
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297 <when value="csv">
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298 <action type="format">
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299 <option type="from_param" name="output_format" />
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300 </action>
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301 </when>
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302 </conditional>
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303 </actions>
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304 </data>
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305 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" >
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306 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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307 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
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308 <actions>
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309 <conditional name="output_format">
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310 <when value="rtable">
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311 <action type="format">
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312 <option type="from_param" name="output_format" />
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313 </action>
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314 </when>
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315 <when value="csv">
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316 <action type="format">
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317 <option type="from_param" name="output_format" />
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318 </action>
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319 </when>
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320 </conditional>
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321 </actions>
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322 </data>
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323 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" >
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324 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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325 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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326 <filter>'sample' in partition_type or not partition_type</filter>
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327 <actions>
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328 <conditional name="output_format">
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329 <when value="rtable">
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330 <action type="format">
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331 <option type="from_param" name="output_format" />
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332 </action>
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333 </when>
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334 <when value="csv">
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335 <action type="format">
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336 <option type="from_param" name="output_format" />
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337 </action>
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338 </when>
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339 </conditional>
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340 </actions>
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341 </data>
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342 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" >
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343 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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344 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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345 <filter>'sample' in partition_type or not partition_type</filter>
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346 <actions>
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347 <conditional name="output_format">
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348 <when value="rtable">
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349 <action type="format">
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350 <option type="from_param" name="output_format" />
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351 </action>
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352 </when>
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353 <when value="csv">
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354 <action type="format">
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355 <option type="from_param" name="output_format" />
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356 </action>
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357 </when>
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358 </conditional>
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359 </actions>
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360 </data>
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361
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362 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
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363 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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364 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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365 <filter>'readgroup' in partition_type</filter>
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366 <actions>
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367 <conditional name="output_format">
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368 <when value="rtable">
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369 <action type="format">
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370 <option type="from_param" name="output_format" />
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371 </action>
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372 </when>
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373 <when value="csv">
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374 <action type="format">
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375 <option type="from_param" name="output_format" />
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376 </action>
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377 </when>
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378 </conditional>
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379 </actions>
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380 </data>
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381 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" >
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382 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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383 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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384 <filter>'readgroup' in partition_type</filter>
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385 <actions>
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386 <conditional name="output_format">
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387 <when value="rtable">
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388 <action type="format">
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389 <option type="from_param" name="output_format" />
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390 </action>
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391 </when>
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392 <when value="csv">
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393 <action type="format">
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394 <option type="from_param" name="output_format" />
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395 </action>
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396 </when>
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397 </conditional>
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398 </actions>
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399 </data>
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400 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" >
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401 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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402 <filter>'readgroup' in partition_type</filter>
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403 <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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404 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
|
|
|
405 <actions>
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406 <conditional name="output_format">
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407 <when value="rtable">
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408 <action type="format">
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|
409 <option type="from_param" name="output_format" />
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410 </action>
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411 </when>
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412 <when value="csv">
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413 <action type="format">
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|
414 <option type="from_param" name="output_format" />
|
|
|
415 </action>
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|
416 </when>
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|
417 </conditional>
|
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418 </actions>
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|
|
419 </data>
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|
|
420 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" >
|
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|
421 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
422 <filter>'readgroup' in partition_type</filter>
|
|
|
423 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
|
|
|
424 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
|
|
|
425 <actions>
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|
426 <conditional name="output_format">
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427 <when value="rtable">
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|
428 <action type="format">
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|
429 <option type="from_param" name="output_format" />
|
|
|
430 </action>
|
|
|
431 </when>
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|
432 <when value="csv">
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|
433 <action type="format">
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|
434 <option type="from_param" name="output_format" />
|
|
|
435 </action>
|
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|
436 </when>
|
|
|
437 </conditional>
|
|
|
438 </actions>
|
|
|
439 </data>
|
|
|
440 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" >
|
|
|
441 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
442 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
|
|
|
443 <actions>
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|
444 <conditional name="output_format">
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|
445 <when value="rtable">
|
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|
446 <action type="format">
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|
447 <option type="from_param" name="output_format" />
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|
448 </action>
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|
|
449 </when>
|
|
|
450 <when value="csv">
|
|
|
451 <action type="format">
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|
|
452 <option type="from_param" name="output_format" />
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|
453 </action>
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|
454 </when>
|
|
|
455 </conditional>
|
|
|
456 </actions>
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|
|
457 </data>
|
|
|
458 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" >
|
|
|
459 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
460 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
|
|
|
461 <actions>
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|
|
462 <conditional name="output_format">
|
|
|
463 <when value="rtable">
|
|
|
464 <action type="format">
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|
|
465 <option type="from_param" name="output_format" />
|
|
|
466 </action>
|
|
|
467 </when>
|
|
|
468 <when value="csv">
|
|
|
469 <action type="format">
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|
|
470 <option type="from_param" name="output_format" />
|
|
|
471 </action>
|
|
|
472 </when>
|
|
|
473 </conditional>
|
|
|
474 </actions>
|
|
|
475 </data>
|
|
|
476 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" >
|
|
|
477 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
478 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
|
|
|
479 <filter>'readgroup' in partition_type</filter>
|
|
|
480 <actions>
|
|
|
481 <conditional name="output_format">
|
|
|
482 <when value="rtable">
|
|
|
483 <action type="format">
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|
|
484 <option type="from_param" name="output_format" />
|
|
|
485 </action>
|
|
|
486 </when>
|
|
|
487 <when value="csv">
|
|
|
488 <action type="format">
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|
|
489 <option type="from_param" name="output_format" />
|
|
|
490 </action>
|
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|
491 </when>
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|
492 </conditional>
|
|
|
493 </actions>
|
|
|
494 </data>
|
|
|
495 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" >
|
|
|
496 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
497 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
|
|
|
498 <filter>'readgroup' in partition_type</filter>
|
|
|
499 <actions>
|
|
|
500 <conditional name="output_format">
|
|
|
501 <when value="rtable">
|
|
|
502 <action type="format">
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|
|
503 <option type="from_param" name="output_format" />
|
|
|
504 </action>
|
|
|
505 </when>
|
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|
506 <when value="csv">
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|
507 <action type="format">
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|
508 <option type="from_param" name="output_format" />
|
|
|
509 </action>
|
|
|
510 </when>
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|
511 </conditional>
|
|
|
512 </actions>
|
|
|
513 </data>
|
|
|
514
|
|
|
515 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
|
|
|
516 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
|
|
|
517 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
518 <filter>'library' in partition_type</filter>
|
|
|
519 <actions>
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|
|
520 <conditional name="output_format">
|
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|
521 <when value="rtable">
|
|
|
522 <action type="format">
|
|
|
523 <option type="from_param" name="output_format" />
|
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|
524 </action>
|
|
|
525 </when>
|
|
|
526 <when value="csv">
|
|
|
527 <action type="format">
|
|
|
528 <option type="from_param" name="output_format" />
|
|
|
529 </action>
|
|
|
530 </when>
|
|
|
531 </conditional>
|
|
|
532 </actions>
|
|
|
533 </data>
|
|
|
534 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" >
|
|
|
535 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
|
|
|
536 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
537 <filter>'library' in partition_type</filter>
|
|
|
538 <actions>
|
|
|
539 <conditional name="output_format">
|
|
|
540 <when value="rtable">
|
|
|
541 <action type="format">
|
|
|
542 <option type="from_param" name="output_format" />
|
|
|
543 </action>
|
|
|
544 </when>
|
|
|
545 <when value="csv">
|
|
|
546 <action type="format">
|
|
|
547 <option type="from_param" name="output_format" />
|
|
|
548 </action>
|
|
|
549 </when>
|
|
|
550 </conditional>
|
|
|
551 </actions>
|
|
|
552 </data>
|
|
|
553 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" >
|
|
|
554 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
555 <filter>'library' in partition_type</filter>
|
|
|
556 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
|
|
|
557 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
|
|
|
558 <actions>
|
|
|
559 <conditional name="output_format">
|
|
|
560 <when value="rtable">
|
|
|
561 <action type="format">
|
|
|
562 <option type="from_param" name="output_format" />
|
|
|
563 </action>
|
|
|
564 </when>
|
|
|
565 <when value="csv">
|
|
|
566 <action type="format">
|
|
|
567 <option type="from_param" name="output_format" />
|
|
|
568 </action>
|
|
|
569 </when>
|
|
|
570 </conditional>
|
|
|
571 </actions>
|
|
|
572 </data>
|
|
|
573 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" >
|
|
|
574 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
575 <filter>'library' in partition_type</filter>
|
|
|
576 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
|
|
|
577 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
|
|
|
578 <actions>
|
|
|
579 <conditional name="output_format">
|
|
|
580 <when value="rtable">
|
|
|
581 <action type="format">
|
|
|
582 <option type="from_param" name="output_format" />
|
|
|
583 </action>
|
|
|
584 </when>
|
|
|
585 <when value="csv">
|
|
|
586 <action type="format">
|
|
|
587 <option type="from_param" name="output_format" />
|
|
|
588 </action>
|
|
|
589 </when>
|
|
|
590 </conditional>
|
|
|
591 </actions>
|
|
|
592 </data>
|
|
|
593 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" >
|
|
|
594 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
595 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
|
|
|
596 <actions>
|
|
|
597 <conditional name="output_format">
|
|
|
598 <when value="rtable">
|
|
|
599 <action type="format">
|
|
|
600 <option type="from_param" name="output_format" />
|
|
|
601 </action>
|
|
|
602 </when>
|
|
|
603 <when value="csv">
|
|
|
604 <action type="format">
|
|
|
605 <option type="from_param" name="output_format" />
|
|
|
606 </action>
|
|
|
607 </when>
|
|
|
608 </conditional>
|
|
|
609 </actions>
|
|
|
610 </data>
|
|
|
611 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" >
|
|
|
612 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
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|
613 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
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614 <actions>
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615 <conditional name="output_format">
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616 <when value="rtable">
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617 <action type="format">
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618 <option type="from_param" name="output_format" />
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619 </action>
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620 </when>
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621 <when value="csv">
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622 <action type="format">
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623 <option type="from_param" name="output_format" />
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624 </action>
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625 </when>
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626 </conditional>
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627 </actions>
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628 </data>
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629 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" >
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630 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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631 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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632 <filter>'library' in partition_type</filter>
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633 <actions>
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634 <conditional name="output_format">
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635 <when value="rtable">
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636 <action type="format">
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637 <option type="from_param" name="output_format" />
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638 </action>
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639 </when>
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640 <when value="csv">
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641 <action type="format">
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642 <option type="from_param" name="output_format" />
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643 </action>
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644 </when>
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645 </conditional>
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646 </actions>
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647 </data>
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648 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" >
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649 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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650 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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|
651 <filter>'library' in partition_type</filter>
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652 <actions>
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653 <conditional name="output_format">
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654 <when value="rtable">
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655 <action type="format">
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656 <option type="from_param" name="output_format" />
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657 </action>
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658 </when>
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659 <when value="csv">
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660 <action type="format">
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661 <option type="from_param" name="output_format" />
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662 </action>
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663 </when>
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664 </conditional>
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665 </actions>
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666 </data>
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667
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668 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
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669 </outputs>
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670 <trackster_conf/>
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671 <tests>
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672 <test>
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673 <param name="reference_source_selector" value="history" />
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674 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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|
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675 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
|
|
|
676 <param name="input_calculate_coverage_over_genes" />
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|
|
677 <param name="partition_type" value="sample" />
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678 <param name="summary_coverage_threshold_group" value="0" />
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|
679 <param name="output_format" value="rtable" />
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|
|
680 <param name="gatk_param_type_selector" value="basic" />
|
|
|
681 <param name="analysis_param_type_selector" value="basic" />
|
|
|
682 <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" />
|
|
|
683 <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" />
|
|
|
684 <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" />
|
|
|
685 <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" />
|
|
|
686 <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" />
|
|
|
687 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" />
|
|
|
688 </test>
|
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|
689 </tests>
|
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|
690 <help>
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|
|
691 **What it does**
|
|
|
692
|
|
|
693 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.
|
|
|
694
|
|
4
|
695 For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html>`_.
|
|
0
|
696
|
|
|
697 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_.
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|
|
698
|
|
|
699 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
|
|
|
700
|
|
|
701 ------
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702
|
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|
703 **Inputs**
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|
|
704
|
|
|
705 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.
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|
|
706
|
|
|
707
|
|
|
708 **Outputs**
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|
|
709
|
|
|
710 The output is in various table formats.
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|
|
711
|
|
|
712
|
|
|
713 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
|
|
|
714
|
|
|
715 -------
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|
|
716
|
|
|
717 **Settings**::
|
|
|
718
|
|
|
719 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
|
|
|
720 ignoreDeletionSites boolean false Ignore sites consisting only of deletions
|
|
|
721 includeDeletions boolean false Include information on deletions
|
|
|
722 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
|
|
|
723 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
|
|
|
724 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
|
|
|
725 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
|
|
|
726 nBins int 499 Number of bins to use for granular binning
|
|
|
727 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
|
|
|
728 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
|
|
|
729 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
|
|
|
730 omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
|
|
|
731 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
|
|
|
732 partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
|
|
|
733 printBaseCounts boolean false Will add base counts to per-locus output.
|
|
|
734 printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
|
|
|
735 start int 1 Starting (left endpoint) for granular binning
|
|
|
736 stop int 500 Ending (right endpoint) for granular binning
|
|
|
737 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
|
|
|
738
|
|
|
739 @CITATION_SECTION@
|
|
|
740 </help>
|
|
4
|
741 <expand macro="citations" />
|
|
0
|
742 </tool>
|
