annotate depth_of_coverage.xml @ 33:76f8ca47b810 draft

Omit --read_filter param included by default
author Jim Johnson <jj@umn.edu>
date Thu, 28 Feb 2013 15:32:04 -0600
parents 6ef8eb568700
children b99c25b0ad4d
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1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.5">
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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="2.3">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 <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 'java
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17 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
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18 -T "DepthOfCoverage"
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19 \$GATK2_SITE_OPTIONS
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6ef8eb568700 Move GATK tool_dependency to a repository dependency, use 2 env vars: GATK2_NUM_THREADS and GATK2_NUM_CPU_THREADS for site threading values
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20 ## \$GATK2_NUM_THREADS
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21 ##--num_threads 4 ##hard coded, for now
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22 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
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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 ##start standard gatk options
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43 #if $gatk_param_type.gatk_param_type_selector == "advanced":
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44 #for $pedigree in $gatk_param_type.pedigree:
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45 -p '--pedigree "${pedigree.pedigree_file}"'
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46 #end for
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47 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
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48 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
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49 #end for
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50 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
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51 #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
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52 #for $read_filter in $gatk_param_type.read_filter:
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53 -p '
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54 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
76f8ca47b810 Omit --read_filter param included by default
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55 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
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56 #end_if
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57 ###raise Exception( str( dir( $read_filter ) ) )
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58 #for $name, $param in $read_filter.read_filter_type.iteritems():
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59 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
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60 #if hasattr( $param.input, 'truevalue' ):
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61 ${param}
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62 #else:
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63 --${name} "${param}"
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64 #end if
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65 #end if
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66 #end for
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67 '
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68 #end for
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69 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
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70 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
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71 #end for
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72
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73 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
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74 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
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75 #end for
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76
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77 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
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78
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79 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
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80 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
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81 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
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82 #end if
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83 -p '
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84 --baq "${gatk_param_type.baq}"
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85 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
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86 ${gatk_param_type.use_original_qualities}
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87 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
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88 --validation_strictness "${gatk_param_type.validation_strictness}"
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89 --interval_merging "${gatk_param_type.interval_merging}"
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90 ${gatk_param_type.disable_experimental_low_memory_sharding}
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91 ${gatk_param_type.fix_misencoded_quality_scores}
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92 ${gatk_param_type.non_deterministic_random_seed}
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93 '
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94 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
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95 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
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96 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
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97 #else
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98 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
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99 #end if
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100 #end for
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101 #end if
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102
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103 #if $reference_source.reference_source_selector == "history":
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104 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
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105 #end if
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106 ##end standard gatk options
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107 ##start analysis specific options
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108 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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109 -p '
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110 ${analysis_param_type.ignore_deletion_sites}
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111 ${analysis_param_type.include_deletions}
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112 --maxBaseQuality "${analysis_param_type.max_base_quality}"
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113 --maxMappingQuality "${analysis_param_type.max_mapping_quality}"
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114 --minBaseQuality "${analysis_param_type.min_base_quality}"
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115 --minMappingQuality "${analysis_param_type.min_mapping_quality}"
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116 --nBins "${analysis_param_type.n_bins}"
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117 ${analysis_param_type.omit_depth_output_at_each_base}
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118 ${analysis_param_type.omit_interval_statistics}
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119 ${analysis_param_type.omit_locus_table}
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120 ${analysis_param_type.omit_per_sample_stats}
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121 ${analysis_param_type.print_base_counts}
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122 ${analysis_param_type.print_bin_endpoints_and_exit}
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123 --start "${analysis_param_type.start}"
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124 --stop "${analysis_param_type.stop}"
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125 '
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126 #end if
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127 ##Move additional files to final location
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128 #if str( $partition_type ) != "None":
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129 #set $partition_types = str( $partition_type ).split( ',' )
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130 #else:
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131 #set $partition_types = [ 'sample' ]
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132 #end if
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133 #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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134 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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135 &amp;&amp; mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
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136 &amp;&amp; mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample}
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137 #end if
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138 #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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139 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
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140 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
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141 #end if
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142 #if str( $input_calculate_coverage_over_genes ) != "None":
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143 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
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144 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample}
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145 #end if
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146 #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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147 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
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148 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
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149 #end if
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150 #end if
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151
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152 #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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153 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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154 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
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155 &amp;&amp; mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
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156 #end if
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157 #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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158 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
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159 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
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160 #end if
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161 #if str( $input_calculate_coverage_over_genes ) != "None":
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162 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
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163 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup}
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164 #end if
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165 #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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jjohnson
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166 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
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jjohnson
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167 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
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jjohnson
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168 #end if
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jjohnson
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169 #end if
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jjohnson
parents:
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170
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jjohnson
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171 #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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jjohnson
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172 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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jjohnson
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173 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
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jjohnson
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174 &amp;&amp; mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
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jjohnson
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175 #end if
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jjohnson
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176 #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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jjohnson
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177 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
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jjohnson
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178 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
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jjohnson
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179 #end if
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jjohnson
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180 #if str( $input_calculate_coverage_over_genes ) != "None":
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jjohnson
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181 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
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jjohnson
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182 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library}
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jjohnson
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183 #end if
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jjohnson
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184 #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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jjohnson
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185 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
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jjohnson
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186 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
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jjohnson
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187 #end if
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jjohnson
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188 #end if
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jjohnson
parents:
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189
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jjohnson
parents:
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190
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jjohnson
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191 </command>
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jjohnson
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192 <inputs>
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jjohnson
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193 <conditional name="reference_source">
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jjohnson
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194 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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jjohnson
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195 <option value="cached">Locally cached</option>
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jjohnson
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196 <option value="history">History</option>
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jjohnson
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197 </param>
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jjohnson
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198 <when value="cached">
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jjohnson
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199 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
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jjohnson
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200 <param name="input_bam" type="data" format="bam" label="BAM file">
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jjohnson
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201 <validator type="unspecified_build" />
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jjohnson
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202 <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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jjohnson
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203 </param>
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jjohnson
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204 </repeat>
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jjohnson
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205 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
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jjohnson
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206 <options from_data_table="gatk2_picard_indexes">
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jjohnson
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207 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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jjohnson
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208 </options>
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jjohnson
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209 <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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jjohnson
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210 </param>
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jjohnson
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211 </when>
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jjohnson
parents:
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212 <when value="history"> <!-- FIX ME!!!! -->
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jjohnson
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213 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
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jjohnson
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214 <param name="input_bam" type="data" format="bam" label="BAM file" />
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jjohnson
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215 </repeat>
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jjohnson
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216 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
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jjohnson
parents:
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217 </when>
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jjohnson
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218 </conditional>
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jjohnson
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219
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220 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />
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jjohnson
parents:
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221
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jjohnson
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222 <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &amp;lt;partitionType&amp;gt;">
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jjohnson
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223 <option value="sample" selected="True">sample</option>
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jjohnson
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224 <option value="readgroup">readgroup</option>
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jjohnson
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225 <option value="library">library</option>
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jjohnson
parents:
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226 </param>
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jjohnson
parents:
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227
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jjohnson
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228 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;">
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jjohnson
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229 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
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jjohnson
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230 </repeat>
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jjohnson
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231
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jjohnson
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232 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" >
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jjohnson
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233 <option value="csv">csv</option>
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jjohnson
parents:
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234 <option value="table">table</option>
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jjohnson
parents:
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235 <option value="rtable" selected="True">rtable</option>
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jjohnson
parents:
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236 </param>
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jjohnson
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237
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jjohnson
parents:
diff changeset
238 <conditional name="gatk_param_type">
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jjohnson
parents:
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239 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
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jjohnson
parents:
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240 <option value="basic" selected="True">Basic</option>
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jjohnson
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241 <option value="advanced">Advanced</option>
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jjohnson
parents:
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242 </param>
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jjohnson
parents:
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243 <when value="basic">
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jjohnson
parents:
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244 <!-- Do nothing here -->
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jjohnson
parents:
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245 </when>
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jjohnson
parents:
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246 <when value="advanced">
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jjohnson
parents:
diff changeset
247 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
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jjohnson
parents:
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248 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
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jjohnson
parents:
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249 </repeat>
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jjohnson
parents:
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250 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
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jjohnson
parents:
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251 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
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jjohnson
parents:
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252 </repeat>
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jjohnson
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253 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
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jjohnson
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254 <option value="STRICT" selected="True">STRICT</option>
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jjohnson
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255 <option value="SILENT">SILENT</option>
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jjohnson
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256 </param>
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jjohnson
parents:
diff changeset
257 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
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jjohnson
parents:
diff changeset
258 <conditional name="read_filter_type">
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jjohnson
parents:
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259 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
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jjohnson
parents:
diff changeset
260 <option value="BadCigar">BadCigar</option>
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jjohnson
parents:
diff changeset
261 <option value="BadMate">BadMate</option>
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jjohnson
parents:
diff changeset
262 <option value="DuplicateRead">DuplicateRead</option>
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jjohnson
parents:
diff changeset
263 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
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jjohnson
parents:
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264 <option value="MalformedRead">MalformedRead</option>
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jjohnson
parents:
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265 <option value="MappingQuality">MappingQuality</option>
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jjohnson
parents:
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266 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
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jjohnson
parents:
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267 <option value="MappingQualityZero">MappingQualityZero</option>
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jjohnson
parents:
diff changeset
268 <option value="MateSameStrand">MateSameStrand</option>
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jjohnson
parents:
diff changeset
269 <option value="MaxInsertSize">MaxInsertSize</option>
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jjohnson
parents:
diff changeset
270 <option value="MaxReadLength" selected="True">MaxReadLength</option>
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jjohnson
parents:
diff changeset
271 <option value="MissingReadGroup">MissingReadGroup</option>
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jjohnson
parents:
diff changeset
272 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
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jjohnson
parents:
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273 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
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jjohnson
parents:
diff changeset
274 <option value="Platform454">Platform454</option>
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jjohnson
parents:
diff changeset
275 <option value="Platform">Platform</option>
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jjohnson
parents:
diff changeset
276 <option value="PlatformUnit">PlatformUnit</option>
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jjohnson
parents:
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277 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
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jjohnson
parents:
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278 <option value="ReadName">ReadName</option>
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jjohnson
parents:
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279 <option value="ReadStrand">ReadStrand</option>
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jjohnson
parents:
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280 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
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jjohnson
parents:
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281 <option value="Sample">Sample</option>
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jjohnson
parents:
diff changeset
282 <option value="SingleReadGroup">SingleReadGroup</option>
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jjohnson
parents:
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283 <option value="UnmappedRead">UnmappedRead</option>
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jjohnson
parents:
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284 </param>
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jjohnson
parents:
diff changeset
285 <when value="BadCigar">
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jjohnson
parents:
diff changeset
286 <!-- no extra options -->
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jjohnson
parents:
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287 </when>
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jjohnson
parents:
diff changeset
288 <when value="BadMate">
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jjohnson
parents:
diff changeset
289 <!-- no extra options -->
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jjohnson
parents:
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290 </when>
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jjohnson
parents:
diff changeset
291 <when value="DuplicateRead">
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jjohnson
parents:
diff changeset
292 <!-- no extra options -->
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jjohnson
parents:
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293 </when>
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jjohnson
parents:
diff changeset
294 <when value="FailsVendorQualityCheck">
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jjohnson
parents:
diff changeset
295 <!-- no extra options -->
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jjohnson
parents:
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296 </when>
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jjohnson
parents:
diff changeset
297 <when value="MalformedRead">
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jjohnson
parents:
diff changeset
298 <!-- no extra options -->
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jjohnson
parents:
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299 </when>
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jjohnson
parents:
diff changeset
300 <when value="MappingQuality">
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jjohnson
parents:
diff changeset
301 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
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jjohnson
parents:
diff changeset
302 </when>
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jjohnson
parents:
diff changeset
303 <when value="MappingQualityUnavailable">
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jjohnson
parents:
diff changeset
304 <!-- no extra options -->
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jjohnson
parents:
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305 </when>
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jjohnson
parents:
diff changeset
306 <when value="MappingQualityZero">
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jjohnson
parents:
diff changeset
307 <!-- no extra options -->
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jjohnson
parents:
diff changeset
308 </when>
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jjohnson
parents:
diff changeset
309 <when value="MateSameStrand">
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jjohnson
parents:
diff changeset
310 <!-- no extra options -->
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jjohnson
parents:
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311 </when>
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jjohnson
parents:
diff changeset
312 <when value="MaxInsertSize">
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jjohnson
parents:
diff changeset
313 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
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jjohnson
parents:
diff changeset
314 </when>
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jjohnson
parents:
diff changeset
315 <when value="MaxReadLength">
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jjohnson
parents:
diff changeset
316 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
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jjohnson
parents:
diff changeset
317 </when>
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jjohnson
parents:
diff changeset
318 <when value="MissingReadGroup">
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jjohnson
parents:
diff changeset
319 <!-- no extra options -->
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jjohnson
parents:
diff changeset
320 </when>
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jjohnson
parents:
diff changeset
321 <when value="NoOriginalQualityScores">
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jjohnson
parents:
diff changeset
322 <!-- no extra options -->
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jjohnson
parents:
diff changeset
323 </when>
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jjohnson
parents:
diff changeset
324 <when value="NotPrimaryAlignment">
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jjohnson
parents:
diff changeset
325 <!-- no extra options -->
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jjohnson
parents:
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326 </when>
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jjohnson
parents:
diff changeset
327 <when value="Platform454">
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jjohnson
parents:
diff changeset
328 <!-- no extra options -->
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jjohnson
parents:
diff changeset
329 </when>
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jjohnson
parents:
diff changeset
330 <when value="Platform">
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jjohnson
parents:
diff changeset
331 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
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jjohnson
parents:
diff changeset
332 </when>
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jjohnson
parents:
diff changeset
333 <when value="PlatformUnit">
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jjohnson
parents:
diff changeset
334 <!-- no extra options -->
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jjohnson
parents:
diff changeset
335 </when>
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jjohnson
parents:
diff changeset
336 <when value="ReadGroupBlackList">
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jjohnson
parents:
diff changeset
337 <!-- no extra options -->
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jjohnson
parents:
diff changeset
338 </when>
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jjohnson
parents:
diff changeset
339 <when value="ReadName">
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jjohnson
parents:
diff changeset
340 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
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jjohnson
parents:
diff changeset
341 </when>
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jjohnson
parents:
diff changeset
342 <when value="ReadStrand">
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jjohnson
parents:
diff changeset
343 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
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jjohnson
parents:
diff changeset
344 </when>
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jjohnson
parents:
diff changeset
345 <when value="ReassignMappingQuality">
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jjohnson
parents:
diff changeset
346 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
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jjohnson
parents:
diff changeset
347 </when>
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jjohnson
parents:
diff changeset
348 <when value="Sample">
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jjohnson
parents:
diff changeset
349 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
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jjohnson
parents:
diff changeset
350 </when>
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jjohnson
parents:
diff changeset
351 <when value="SingleReadGroup">
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jjohnson
parents:
diff changeset
352 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
353 </when>
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jjohnson
parents:
diff changeset
354 <when value="UnmappedRead">
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jjohnson
parents:
diff changeset
355 <!-- no extra options -->
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jjohnson
parents:
diff changeset
356 </when>
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jjohnson
parents:
diff changeset
357 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
358 </repeat>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
359 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
360 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
361 </repeat>
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jjohnson
parents:
diff changeset
362 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
363 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
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jjohnson
parents:
diff changeset
364 </repeat>
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jjohnson
parents:
diff changeset
365
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jjohnson
parents:
diff changeset
366 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
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jjohnson
parents:
diff changeset
367 <option value="UNION" selected="True">UNION</option>
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jjohnson
parents:
diff changeset
368 <option value="INTERSECTION">INTERSECTION</option>
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jjohnson
parents:
diff changeset
369 </param>
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jjohnson
parents:
diff changeset
370
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jjohnson
parents:
diff changeset
371 <conditional name="downsampling_type">
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jjohnson
parents:
diff changeset
372 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
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jjohnson
parents:
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373 <option value="NONE" selected="True">NONE</option>
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jjohnson
parents:
diff changeset
374 <option value="ALL_READS">ALL_READS</option>
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jjohnson
parents:
diff changeset
375 <option value="BY_SAMPLE">BY_SAMPLE</option>
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jjohnson
parents:
diff changeset
376 </param>
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jjohnson
parents:
diff changeset
377 <when value="NONE">
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jjohnson
parents:
diff changeset
378 <!-- no more options here -->
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jjohnson
parents:
diff changeset
379 </when>
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jjohnson
parents:
diff changeset
380 <when value="ALL_READS">
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jjohnson
parents:
diff changeset
381 <conditional name="downsample_to_type">
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jjohnson
parents:
diff changeset
382 <param name="downsample_to_type_selector" type="select" label="Downsample method">
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jjohnson
parents:
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383 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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jjohnson
parents:
diff changeset
384 <option value="downsample_to_coverage">Downsample by Coverage</option>
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jjohnson
parents:
diff changeset
385 </param>
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jjohnson
parents:
diff changeset
386 <when value="downsample_to_fraction">
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jjohnson
parents:
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387 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
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jjohnson
parents:
diff changeset
388 </when>
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jjohnson
parents:
diff changeset
389 <when value="downsample_to_coverage">
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jjohnson
parents:
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390 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
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jjohnson
parents:
diff changeset
391 </when>
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jjohnson
parents:
diff changeset
392 </conditional>
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jjohnson
parents:
diff changeset
393 </when>
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jjohnson
parents:
diff changeset
394 <when value="BY_SAMPLE">
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jjohnson
parents:
diff changeset
395 <conditional name="downsample_to_type">
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jjohnson
parents:
diff changeset
396 <param name="downsample_to_type_selector" type="select" label="Downsample method">
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jjohnson
parents:
diff changeset
397 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
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jjohnson
parents:
diff changeset
398 <option value="downsample_to_coverage">Downsample by Coverage</option>
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jjohnson
parents:
diff changeset
399 </param>
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jjohnson
parents:
diff changeset
400 <when value="downsample_to_fraction">
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jjohnson
parents:
diff changeset
401 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
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jjohnson
parents:
diff changeset
402 </when>
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jjohnson
parents:
diff changeset
403 <when value="downsample_to_coverage">
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jjohnson
parents:
diff changeset
404 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
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jjohnson
parents:
diff changeset
405 </when>
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jjohnson
parents:
diff changeset
406 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
407 </when>
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jjohnson
parents:
diff changeset
408 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
409 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
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jjohnson
parents:
diff changeset
410 <option value="OFF" selected="True">OFF</option>
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jjohnson
parents:
diff changeset
411 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
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jjohnson
parents:
diff changeset
412 <option value="RECALCULATE">RECALCULATE</option>
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jjohnson
parents:
diff changeset
413 </param>
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jjohnson
parents:
diff changeset
414 <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
415 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
416 <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
417 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
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jjohnson
parents:
diff changeset
418 <option value="STRICT" selected="True">STRICT</option>
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jjohnson
parents:
diff changeset
419 <option value="LENIENT">LENIENT</option>
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jjohnson
parents:
diff changeset
420 <option value="SILENT">SILENT</option>
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jjohnson
parents:
diff changeset
421 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
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jjohnson
parents:
diff changeset
422 </param>
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jjohnson
parents:
diff changeset
423 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
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jjohnson
parents:
diff changeset
424 <option value="ALL" selected="True">ALL</option>
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jjohnson
parents:
diff changeset
425 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
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jjohnson
parents:
diff changeset
426 </param>
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jjohnson
parents:
diff changeset
427
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jjohnson
parents:
diff changeset
428 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
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jjohnson
parents:
diff changeset
429 <conditional name="read_group_black_list_type">
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jjohnson
parents:
diff changeset
430 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
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jjohnson
parents:
diff changeset
431 <option value="file" selected="True">Filters in file</option>
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jjohnson
parents:
diff changeset
432 <option value="text">Specify filters as a string</option>
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jjohnson
parents:
diff changeset
433 </param>
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jjohnson
parents:
diff changeset
434 <when value="file">
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jjohnson
parents:
diff changeset
435 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
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jjohnson
parents:
diff changeset
436 </when>
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jjohnson
parents:
diff changeset
437 <when value="text">
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jjohnson
parents:
diff changeset
438 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
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jjohnson
parents:
diff changeset
439 </when>
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jjohnson
parents:
diff changeset
440 </conditional>
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jjohnson
parents:
diff changeset
441 </repeat>
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jjohnson
parents:
diff changeset
442
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jjohnson
parents:
diff changeset
443 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
444 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
18
7533db8dfb5b Update tool_dependencies to GATK v 2.3
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
445 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
0
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jjohnson
parents:
diff changeset
446
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jjohnson
parents:
diff changeset
447 </when>
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jjohnson
parents:
diff changeset
448 </conditional>
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jjohnson
parents:
diff changeset
449
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jjohnson
parents:
diff changeset
450 <conditional name="analysis_param_type">
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jjohnson
parents:
diff changeset
451 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
452 <option value="basic" selected="True">Basic</option>
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jjohnson
parents:
diff changeset
453 <option value="advanced">Advanced</option>
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jjohnson
parents:
diff changeset
454 </param>
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jjohnson
parents:
diff changeset
455 <when value="basic">
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jjohnson
parents:
diff changeset
456 <!-- Do nothing here -->
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jjohnson
parents:
diff changeset
457 </when>
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jjohnson
parents:
diff changeset
458 <when value="advanced">
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jjohnson
parents:
diff changeset
459 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
460 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
461 <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &amp;lt;maxBaseQuality&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
462 <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &amp;lt;minBaseQuality&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
463 <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &amp;lt;maxMappingQuality&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
464 <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality &amp;lt;minMappingQuality&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
465 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &amp;lt;nBins&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
466 <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" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
467 <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
468 <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" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
469 <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
470 <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
471 <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
472 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &amp;lt;start&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
473 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;gt;" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
474 </when>
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jjohnson
parents:
diff changeset
475 </conditional>
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jjohnson
parents:
diff changeset
476 </inputs>
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jjohnson
parents:
diff changeset
477 <outputs>
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jjohnson
parents:
diff changeset
478 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
479 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
480 <actions>
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jjohnson
parents:
diff changeset
481 <conditional name="output_format">
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jjohnson
parents:
diff changeset
482 <when value="rtable">
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jjohnson
parents:
diff changeset
483 <action type="format">
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jjohnson
parents:
diff changeset
484 <option type="from_param" name="output_format" />
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jjohnson
parents:
diff changeset
485 </action>
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jjohnson
parents:
diff changeset
486 </when>
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jjohnson
parents:
diff changeset
487 <when value="csv">
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jjohnson
parents:
diff changeset
488 <action type="format">
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jjohnson
parents:
diff changeset
489 <option type="from_param" name="output_format" />
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jjohnson
parents:
diff changeset
490 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
491 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
492 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
493 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
494 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
495 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
496 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
497 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
498 <filter>'sample' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
499 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
500 <conditional name="output_format">
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jjohnson
parents:
diff changeset
501 <when value="rtable">
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jjohnson
parents:
diff changeset
502 <action type="format">
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jjohnson
parents:
diff changeset
503 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
504 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
505 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
506 <when value="csv">
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jjohnson
parents:
diff changeset
507 <action type="format">
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jjohnson
parents:
diff changeset
508 <option type="from_param" name="output_format" />
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jjohnson
parents:
diff changeset
509 </action>
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jjohnson
parents:
diff changeset
510 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
511 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
512 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
513 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
514 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
515 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
516 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
517 <filter>'sample' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
518 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
519 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
520 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
521 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
522 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
523 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
524 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
525 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
526 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
527 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
528 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
529 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
530 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
531 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
532 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
533 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
534 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
535 <filter>'sample' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
536 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
537 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
538 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
539 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
540 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
541 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
542 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
543 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
544 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
545 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
546 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
547 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
548 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
549 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
550 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
551 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
552 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
553 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
554 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
555 <filter>'sample' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
556 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
557 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
558 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
559 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
560 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
561 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
562 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
563 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
564 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
565 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
566 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
567 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
568 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
569 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
570 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
571 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
572 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
573 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
574 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
575 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
576 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
577 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
578 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
579 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
580 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
581 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
582 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
583 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
584 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
585 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
586 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
587 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
588 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
589 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
590 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
591 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
592 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
593 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
594 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
595 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
596 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
597 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
598 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
599 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
600 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
601 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
602 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
603 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
604 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
605 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
606 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
607 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
608 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
609 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
610 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
611 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
612 <filter>'sample' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
613 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
614 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
615 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
616 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
617 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
618 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
619 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
620 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
621 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
622 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
623 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
624 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
625 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
626 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
627 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
628 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
629 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
630 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
631 <filter>'sample' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
632 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
633 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
634 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
635 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
636 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
637 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
638 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
639 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
640 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
641 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
642 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
643 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
644 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
645 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
646 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
647
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
648 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
649 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
650 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
651 <filter>'readgroup' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
652 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
653 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
654 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
655 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
656 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
657 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
658 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
659 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
660 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
661 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
662 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
663 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
664 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
665 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
666 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
667 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
668 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
669 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
670 <filter>'readgroup' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
671 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
672 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
673 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
674 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
675 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
676 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
677 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
678 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
679 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
680 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
681 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
682 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
683 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
684 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
685 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
686 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
687 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
688 <filter>'readgroup' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
689 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
690 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
691 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
692 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
693 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
694 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
695 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
696 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
697 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
698 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
699 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
700 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
701 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
702 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
703 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
704 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
705 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
706 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
707 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
708 <filter>'readgroup' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
709 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
710 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
711 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
712 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
713 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
714 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
715 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
716 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
717 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
718 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
719 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
720 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
721 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
722 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
723 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
724 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
725 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
726 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
727 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
728 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
729 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
730 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
731 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
732 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
733 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
734 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
735 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
736 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
737 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
738 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
739 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
740 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
741 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
742 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
743 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
744 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
745 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
746 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
747 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
748 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
749 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
750 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
751 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
752 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
753 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
754 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
755 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
756 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
757 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
758 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
759 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
760 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
761 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
762 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
763 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
764 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
765 <filter>'readgroup' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
766 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
767 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
768 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
769 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
770 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
771 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
772 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
773 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
774 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
775 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
776 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
777 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
778 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
779 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
780 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
781 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
782 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
783 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
784 <filter>'readgroup' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
785 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
786 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
787 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
788 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
789 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
790 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
791 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
792 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
793 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
794 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
795 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
796 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
797 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
798 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
799 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
800
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
801 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
802 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
803 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
804 <filter>'library' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
805 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
806 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
807 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
808 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
809 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
810 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
811 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
812 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
813 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
814 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
815 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
816 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
817 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
818 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
819 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
820 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
821 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
822 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
823 <filter>'library' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
824 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
825 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
826 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
827 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
828 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
829 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
830 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
831 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
832 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
833 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
834 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
835 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
836 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
837 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
838 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
839 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
840 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
841 <filter>'library' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
842 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
843 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
844 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
845 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
846 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
847 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
848 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
849 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
850 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
851 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
852 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
853 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
854 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
855 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
856 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
857 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
858 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
859 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
860 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
861 <filter>'library' in partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
862 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
863 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
864 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
865 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
866 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
867 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
868 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
869 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
870 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
871 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
872 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
873 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
874 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
875 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
876 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
877 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
878 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
879 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" >
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
880 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
881 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
882 <actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
883 <conditional name="output_format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
884 <when value="rtable">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
885 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
886 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
887 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
888 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
889 <when value="csv">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
890 <action type="format">
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
891 <option type="from_param" name="output_format" />
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
892 </action>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
893 </when>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
894 </conditional>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
895 </actions>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
896 </data>
74c05070a3f8 Uploaded
jjohnson
parents:
diff changeset
897 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" >
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diff changeset
898 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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jjohnson
parents:
diff changeset
899 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
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jjohnson
parents:
diff changeset
900 <actions>
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jjohnson
parents:
diff changeset
901 <conditional name="output_format">
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parents:
diff changeset
902 <when value="rtable">
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jjohnson
parents:
diff changeset
903 <action type="format">
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jjohnson
parents:
diff changeset
904 <option type="from_param" name="output_format" />
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jjohnson
parents:
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905 </action>
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jjohnson
parents:
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906 </when>
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jjohnson
parents:
diff changeset
907 <when value="csv">
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jjohnson
parents:
diff changeset
908 <action type="format">
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jjohnson
parents:
diff changeset
909 <option type="from_param" name="output_format" />
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jjohnson
parents:
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910 </action>
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parents:
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911 </when>
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jjohnson
parents:
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912 </conditional>
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jjohnson
parents:
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913 </actions>
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914 </data>
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jjohnson
parents:
diff changeset
915 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" >
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jjohnson
parents:
diff changeset
916 <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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parents:
diff changeset
917 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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jjohnson
parents:
diff changeset
918 <filter>'library' in partition_type</filter>
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jjohnson
parents:
diff changeset
919 <actions>
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jjohnson
parents:
diff changeset
920 <conditional name="output_format">
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parents:
diff changeset
921 <when value="rtable">
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parents:
diff changeset
922 <action type="format">
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jjohnson
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diff changeset
923 <option type="from_param" name="output_format" />
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924 </action>
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diff changeset
925 </when>
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jjohnson
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diff changeset
926 <when value="csv">
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parents:
diff changeset
927 <action type="format">
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928 <option type="from_param" name="output_format" />
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929 </action>
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930 </when>
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931 </conditional>
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932 </actions>
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jjohnson
parents:
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933 </data>
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parents:
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934 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" >
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parents:
diff changeset
935 <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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parents:
diff changeset
936 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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parents:
diff changeset
937 <filter>'library' in partition_type</filter>
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parents:
diff changeset
938 <actions>
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jjohnson
parents:
diff changeset
939 <conditional name="output_format">
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parents:
diff changeset
940 <when value="rtable">
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jjohnson
parents:
diff changeset
941 <action type="format">
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jjohnson
parents:
diff changeset
942 <option type="from_param" name="output_format" />
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jjohnson
parents:
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943 </action>
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jjohnson
parents:
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944 </when>
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jjohnson
parents:
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945 <when value="csv">
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jjohnson
parents:
diff changeset
946 <action type="format">
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jjohnson
parents:
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947 <option type="from_param" name="output_format" />
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jjohnson
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948 </action>
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949 </when>
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950 </conditional>
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951 </actions>
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jjohnson
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diff changeset
952 </data>
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parents:
diff changeset
953
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parents:
diff changeset
954 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
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955 </outputs>
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jjohnson
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diff changeset
956 <trackster_conf/>
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jjohnson
parents:
diff changeset
957 <tests>
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parents:
diff changeset
958 <test>
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parents:
diff changeset
959 <param name="reference_source_selector" value="history" />
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jjohnson
parents:
diff changeset
960 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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jjohnson
parents:
diff changeset
961 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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parents:
diff changeset
962 <param name="input_calculate_coverage_over_genes" />
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jjohnson
parents:
diff changeset
963 <param name="partition_type" value="sample" />
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jjohnson
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diff changeset
964 <param name="summary_coverage_threshold_group" value="0" />
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jjohnson
parents:
diff changeset
965 <param name="output_format" value="rtable" />
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jjohnson
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diff changeset
966 <param name="gatk_param_type_selector" value="basic" />
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parents:
diff changeset
967 <param name="analysis_param_type_selector" value="basic" />
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parents:
diff changeset
968 <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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parents:
diff changeset
969 <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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diff changeset
970 <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" />
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jjohnson
parents:
diff changeset
971 <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" />
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jjohnson
parents:
diff changeset
972 <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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jjohnson
parents:
diff changeset
973 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" />
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jjohnson
parents:
diff changeset
974 </test>
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jjohnson
parents:
diff changeset
975 </tests>
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jjohnson
parents:
diff changeset
976 <help>
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jjohnson
parents:
diff changeset
977 **What it does**
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978
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jjohnson
parents:
diff changeset
979 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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jjohnson
parents:
diff changeset
980
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jjohnson
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diff changeset
981 For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html&gt;`_.
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jjohnson
parents:
diff changeset
982
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jjohnson
parents:
diff changeset
983 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
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jjohnson
parents:
diff changeset
984
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jjohnson
parents:
diff changeset
985 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
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jjohnson
parents:
diff changeset
986
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987 ------
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jjohnson
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diff changeset
988
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jjohnson
parents:
diff changeset
989 **Inputs**
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jjohnson
parents:
diff changeset
990
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jjohnson
parents:
diff changeset
991 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.
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jjohnson
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diff changeset
992
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jjohnson
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993
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jjohnson
parents:
diff changeset
994 **Outputs**
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diff changeset
995
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996 The output is in various table formats.
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997
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998
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999 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
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1000
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jjohnson
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diff changeset
1001 -------
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jjohnson
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diff changeset
1002
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jjohnson
parents:
diff changeset
1003 **Settings**::
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diff changeset
1004
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1005 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
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diff changeset
1006 ignoreDeletionSites boolean false Ignore sites consisting only of deletions
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1007 includeDeletions boolean false Include information on deletions
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1008 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
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1009 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
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parents:
diff changeset
1010 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
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1011 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
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1012 nBins int 499 Number of bins to use for granular binning
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1013 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
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1014 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
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parents:
diff changeset
1015 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
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1016 omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
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1017 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
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1018 partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
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parents:
diff changeset
1019 printBaseCounts boolean false Will add base counts to per-locus output.
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diff changeset
1020 printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
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jjohnson
parents:
diff changeset
1021 start int 1 Starting (left endpoint) for granular binning
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1022 stop int 500 Ending (right endpoint) for granular binning
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diff changeset
1023 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
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diff changeset
1024
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diff changeset
1025 ------
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diff changeset
1026
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jjohnson
parents:
diff changeset
1027 **Citation**
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diff changeset
1028
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diff changeset
1029 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_
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1030
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diff changeset
1031 Please also site `McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. Epub 2010 Jul 19. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20644199&gt;`_
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diff changeset
1032
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diff changeset
1033 If you use this tool in Galaxy, please cite `Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20069535&gt;`_
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diff changeset
1034
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1035 </help>
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diff changeset
1036 </tool>