annotate depth_of_coverage.xml @ 6:35c00763cb5c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
author iuc
date Mon, 04 Jun 2018 05:38:15 -0400
parents f244b8209eb8
children
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35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1">
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2 <description>on BAM files</description>
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3 <macros>
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4 <import>gatk2_macros.xml</import>
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5 </macros>
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35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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6 <expand macro="requirements" />
35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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7 <expand macro="version_command" />
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8 <command interpreter="python">gatk2_wrapper.py
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9 ##--max_jvm_heap_fraction "1"
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10 --stdout "${output_log}"
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35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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11 @BAM_INPUTS@
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12 -p '
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13 @JAR_PATH@
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14 -T "DepthOfCoverage"
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15 \$GATK2_SITE_OPTIONS
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16
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17 @THREADS@
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18
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19 #if $reference_source.reference_source_selector != "history":
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20 -R "${reference_source.ref_file.fields.path}"
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21 #end if
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22 #if str( $input_calculate_coverage_over_genes ) != "None":
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23 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}"
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24 #end if
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25 #if str( $partition_type ) != "None":
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26 #for $pt in str( $partition_type ).split( ',' ):
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27 --partitionType "${pt}"
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28 #end for
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29 #end if
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30 --out "${output_per_locus_coverage}"
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35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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31
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32 #for $ct_group in $summary_coverage_threshold_group:
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33 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
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34 #end for
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35 --outputFormat "${output_format}"
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36 '
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35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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37
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38 #include source=$standard_gatk_options#
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39 ##start analysis specific options
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40 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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41 -p '
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42 ${analysis_param_type.ignore_deletion_sites}
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43 ${analysis_param_type.include_deletions}
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44 --maxBaseQuality "${analysis_param_type.max_base_quality}"
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45 --maxMappingQuality "${analysis_param_type.max_mapping_quality}"
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46 --minBaseQuality "${analysis_param_type.min_base_quality}"
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47 --minMappingQuality "${analysis_param_type.min_mapping_quality}"
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48 --nBins "${analysis_param_type.n_bins}"
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49 ${analysis_param_type.omit_depth_output_at_each_base}
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50 ${analysis_param_type.omit_interval_statistics}
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51 ${analysis_param_type.omit_locus_table}
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52 ${analysis_param_type.omit_per_sample_stats}
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53 ${analysis_param_type.print_base_counts}
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54 ${analysis_param_type.print_bin_endpoints_and_exit}
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55 --start "${analysis_param_type.start}"
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56 --stop "${analysis_param_type.stop}"
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57 '
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58 #end if
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59 ##Move additional files to final location
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60 #if str( $partition_type ) != "None":
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61 #set $partition_types = str( $partition_type ).split( ',' )
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62 #else:
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63 #set $partition_types = [ 'sample' ]
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64 #end if
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65 #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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66 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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67 &amp;&amp; mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
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68 &amp;&amp; mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample}
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69 #end if
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70 #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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71 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
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72 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
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73 #end if
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74 #if str( $input_calculate_coverage_over_genes ) != "None":
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75 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
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76 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample}
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77 #end if
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78 #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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79 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
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80 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
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81 #end if
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82 #end if
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83
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84 #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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85 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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86 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
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87 &amp;&amp; mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
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88 #end if
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89 #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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90 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
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91 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
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92 #end if
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93 #if str( $input_calculate_coverage_over_genes ) != "None":
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94 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
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95 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup}
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96 #end if
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97 #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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98 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
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99 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
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100 #end if
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101 #end if
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102
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103 #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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104 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
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105 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
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106 &amp;&amp; mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
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107 #end if
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108 #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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109 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
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110 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
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111 #end if
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112 #if str( $input_calculate_coverage_over_genes ) != "None":
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113 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
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114 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library}
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115 #end if
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116 #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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117 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
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118 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
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119 #end if
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120 #end if
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121
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122 </command>
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123 <inputs>
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124 <conditional name="reference_source">
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125 <expand macro="reference_source_selector_param" />
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126 <when value="cached">
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127 <expand macro="input_bams_cached" />
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128 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
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129 <options from_data_table="gatk2_picard_indexes">
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130 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
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131 </options>
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132 <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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133 </param>
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134 </when>
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135 <when value="history"> <!-- FIX ME!!!! -->
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137 <expand macro="input_bams_history" />
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138 <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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139 </when>
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140 </conditional>
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141
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142 <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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143
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144 <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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145 <option value="sample" selected="True">sample</option>
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146 <option value="readgroup">readgroup</option>
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147 <option value="library">library</option>
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148 </param>
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149
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150 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;">
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151 <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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152 </repeat>
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35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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153
0
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154 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" >
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155 <option value="csv">csv</option>
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156 <option value="table">table</option>
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157 <option value="rtable" selected="True">rtable</option>
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158 </param>
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35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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159
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160 <expand macro="gatk_param_type_conditional" />
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161
0
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162 <expand macro="analysis_type_conditional">
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163 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
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164 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
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165 <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;" />
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166 <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;" />
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167 <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;" />
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168 <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;" />
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169 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &amp;lt;nBins&amp;gt;" />
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170 <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" help="-omitBaseOutput,--omitDepthOutputAtEachBase" />
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171 <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" />
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172 <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" help="-omitLocusTable,--omitLocusTable" />
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173 <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" />
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174 <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" />
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175 <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
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176 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &amp;lt;start&amp;gt;" />
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177 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;gt;" />
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178 </expand>
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179 </inputs>
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180 <outputs>
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181 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
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182 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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183 <actions>
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184 <conditional name="output_format">
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185 <when value="rtable">
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186 <action type="format">
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187 <option type="from_param" name="output_format" />
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188 </action>
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189 </when>
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190 <when value="csv">
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191 <action type="format">
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192 <option type="from_param" name="output_format" />
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193 </action>
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194 </when>
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195 </conditional>
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196 </actions>
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197 </data>
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198 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" >
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199 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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200 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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201 <filter>'sample' in partition_type or not partition_type</filter>
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202 <actions>
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203 <conditional name="output_format">
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204 <when value="rtable">
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205 <action type="format">
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206 <option type="from_param" name="output_format" />
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207 </action>
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208 </when>
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209 <when value="csv">
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210 <action type="format">
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211 <option type="from_param" name="output_format" />
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212 </action>
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213 </when>
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214 </conditional>
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215 </actions>
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216 </data>
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217 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" >
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218 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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219 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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220 <filter>'sample' in partition_type or not partition_type</filter>
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221 <actions>
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222 <conditional name="output_format">
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223 <when value="rtable">
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224 <action type="format">
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225 <option type="from_param" name="output_format" />
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226 </action>
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227 </when>
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228 <when value="csv">
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229 <action type="format">
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230 <option type="from_param" name="output_format" />
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231 </action>
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232 </when>
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233 </conditional>
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234 </actions>
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235 </data>
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236 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" >
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237 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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238 <filter>'sample' in partition_type or not partition_type</filter>
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239 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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240 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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241 <actions>
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242 <conditional name="output_format">
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243 <when value="rtable">
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244 <action type="format">
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245 <option type="from_param" name="output_format" />
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246 </action>
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247 </when>
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248 <when value="csv">
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249 <action type="format">
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250 <option type="from_param" name="output_format" />
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251 </action>
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252 </when>
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253 </conditional>
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254 </actions>
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255 </data>
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256 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" >
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257 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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258 <filter>'sample' in partition_type or not partition_type</filter>
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259 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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260 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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261 <actions>
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262 <conditional name="output_format">
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263 <when value="rtable">
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264 <action type="format">
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265 <option type="from_param" name="output_format" />
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266 </action>
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267 </when>
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268 <when value="csv">
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269 <action type="format">
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270 <option type="from_param" name="output_format" />
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271 </action>
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272 </when>
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273 </conditional>
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274 </actions>
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275 </data>
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276 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" >
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277 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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278 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
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279 <actions>
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280 <conditional name="output_format">
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281 <when value="rtable">
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282 <action type="format">
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283 <option type="from_param" name="output_format" />
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284 </action>
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285 </when>
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286 <when value="csv">
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287 <action type="format">
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288 <option type="from_param" name="output_format" />
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289 </action>
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290 </when>
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291 </conditional>
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292 </actions>
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293 </data>
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294 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" >
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295 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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296 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
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297 <actions>
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298 <conditional name="output_format">
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299 <when value="rtable">
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300 <action type="format">
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301 <option type="from_param" name="output_format" />
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302 </action>
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303 </when>
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304 <when value="csv">
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305 <action type="format">
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306 <option type="from_param" name="output_format" />
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307 </action>
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308 </when>
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309 </conditional>
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310 </actions>
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311 </data>
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312 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" >
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313 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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314 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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315 <filter>'sample' in partition_type or not partition_type</filter>
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316 <actions>
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317 <conditional name="output_format">
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318 <when value="rtable">
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319 <action type="format">
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320 <option type="from_param" name="output_format" />
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321 </action>
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322 </when>
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323 <when value="csv">
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324 <action type="format">
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325 <option type="from_param" name="output_format" />
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326 </action>
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327 </when>
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328 </conditional>
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329 </actions>
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330 </data>
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331 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" >
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332 <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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333 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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334 <filter>'sample' in partition_type or not partition_type</filter>
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335 <actions>
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336 <conditional name="output_format">
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337 <when value="rtable">
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338 <action type="format">
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339 <option type="from_param" name="output_format" />
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340 </action>
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341 </when>
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342 <when value="csv">
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343 <action type="format">
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344 <option type="from_param" name="output_format" />
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345 </action>
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346 </when>
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347 </conditional>
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348 </actions>
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349 </data>
6
35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 4
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350
0
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351 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
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352 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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353 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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354 <filter>'readgroup' in partition_type</filter>
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355 <actions>
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356 <conditional name="output_format">
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357 <when value="rtable">
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358 <action type="format">
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359 <option type="from_param" name="output_format" />
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360 </action>
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361 </when>
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362 <when value="csv">
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363 <action type="format">
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364 <option type="from_param" name="output_format" />
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365 </action>
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366 </when>
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367 </conditional>
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368 </actions>
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369 </data>
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370 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" >
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371 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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372 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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373 <filter>'readgroup' in partition_type</filter>
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374 <actions>
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375 <conditional name="output_format">
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376 <when value="rtable">
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377 <action type="format">
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378 <option type="from_param" name="output_format" />
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379 </action>
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380 </when>
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381 <when value="csv">
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382 <action type="format">
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383 <option type="from_param" name="output_format" />
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384 </action>
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385 </when>
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386 </conditional>
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387 </actions>
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388 </data>
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389 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" >
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390 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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391 <filter>'readgroup' in partition_type</filter>
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392 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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393 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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394 <actions>
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395 <conditional name="output_format">
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396 <when value="rtable">
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397 <action type="format">
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398 <option type="from_param" name="output_format" />
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399 </action>
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400 </when>
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401 <when value="csv">
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402 <action type="format">
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403 <option type="from_param" name="output_format" />
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404 </action>
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405 </when>
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406 </conditional>
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407 </actions>
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408 </data>
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409 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" >
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410 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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411 <filter>'readgroup' in partition_type</filter>
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412 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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413 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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414 <actions>
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415 <conditional name="output_format">
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416 <when value="rtable">
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417 <action type="format">
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418 <option type="from_param" name="output_format" />
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419 </action>
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420 </when>
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421 <when value="csv">
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422 <action type="format">
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423 <option type="from_param" name="output_format" />
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424 </action>
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425 </when>
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426 </conditional>
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427 </actions>
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428 </data>
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429 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" >
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parents:
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430 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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parents:
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431 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
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432 <actions>
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433 <conditional name="output_format">
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434 <when value="rtable">
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435 <action type="format">
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436 <option type="from_param" name="output_format" />
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437 </action>
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438 </when>
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439 <when value="csv">
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440 <action type="format">
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441 <option type="from_param" name="output_format" />
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442 </action>
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443 </when>
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444 </conditional>
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445 </actions>
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446 </data>
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447 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" >
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448 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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parents:
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449 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
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450 <actions>
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451 <conditional name="output_format">
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452 <when value="rtable">
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453 <action type="format">
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454 <option type="from_param" name="output_format" />
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455 </action>
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456 </when>
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457 <when value="csv">
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458 <action type="format">
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459 <option type="from_param" name="output_format" />
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460 </action>
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461 </when>
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462 </conditional>
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463 </actions>
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464 </data>
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465 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" >
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466 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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467 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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parents:
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468 <filter>'readgroup' in partition_type</filter>
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469 <actions>
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470 <conditional name="output_format">
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471 <when value="rtable">
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472 <action type="format">
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473 <option type="from_param" name="output_format" />
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474 </action>
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475 </when>
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476 <when value="csv">
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477 <action type="format">
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478 <option type="from_param" name="output_format" />
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479 </action>
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480 </when>
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481 </conditional>
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482 </actions>
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483 </data>
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484 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" >
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parents:
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485 <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:
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486 <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:
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487 <filter>'readgroup' in partition_type</filter>
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488 <actions>
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489 <conditional name="output_format">
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490 <when value="rtable">
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491 <action type="format">
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492 <option type="from_param" name="output_format" />
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493 </action>
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494 </when>
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495 <when value="csv">
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496 <action type="format">
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497 <option type="from_param" name="output_format" />
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498 </action>
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499 </when>
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500 </conditional>
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501 </actions>
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502 </data>
6
35c00763cb5c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents: 4
diff changeset
503
0
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parents:
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504 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
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parents:
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505 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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parents:
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506 <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:
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507 <filter>'library' in partition_type</filter>
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parents:
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508 <actions>
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parents:
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509 <conditional name="output_format">
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510 <when value="rtable">
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parents:
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511 <action type="format">
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parents:
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512 <option type="from_param" name="output_format" />
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513 </action>
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514 </when>
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515 <when value="csv">
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516 <action type="format">
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parents:
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517 <option type="from_param" name="output_format" />
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518 </action>
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519 </when>
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520 </conditional>
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521 </actions>
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522 </data>
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parents:
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523 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" >
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parents:
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524 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
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parents:
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525 <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:
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526 <filter>'library' in partition_type</filter>
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527 <actions>
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528 <conditional name="output_format">
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529 <when value="rtable">
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530 <action type="format">
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531 <option type="from_param" name="output_format" />
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532 </action>
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533 </when>
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534 <when value="csv">
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parents:
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535 <action type="format">
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536 <option type="from_param" name="output_format" />
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537 </action>
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538 </when>
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parents:
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539 </conditional>
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parents:
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540 </actions>
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parents:
diff changeset
541 </data>
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parents:
diff changeset
542 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" >
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diff changeset
543 <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
544 <filter>'library' in partition_type</filter>
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parents:
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545 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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parents:
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546 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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parents:
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547 <actions>
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548 <conditional name="output_format">
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549 <when value="rtable">
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550 <action type="format">
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551 <option type="from_param" name="output_format" />
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552 </action>
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553 </when>
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554 <when value="csv">
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555 <action type="format">
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556 <option type="from_param" name="output_format" />
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557 </action>
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558 </when>
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559 </conditional>
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560 </actions>
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561 </data>
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562 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" >
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563 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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564 <filter>'library' in partition_type</filter>
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565 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
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diff changeset
566 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
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567 <actions>
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568 <conditional name="output_format">
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569 <when value="rtable">
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570 <action type="format">
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571 <option type="from_param" name="output_format" />
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572 </action>
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573 </when>
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574 <when value="csv">
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575 <action type="format">
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576 <option type="from_param" name="output_format" />
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577 </action>
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578 </when>
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579 </conditional>
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580 </actions>
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581 </data>
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582 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" >
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583 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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584 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
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585 <actions>
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586 <conditional name="output_format">
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587 <when value="rtable">
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588 <action type="format">
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589 <option type="from_param" name="output_format" />
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590 </action>
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591 </when>
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592 <when value="csv">
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593 <action type="format">
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594 <option type="from_param" name="output_format" />
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595 </action>
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596 </when>
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597 </conditional>
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598 </actions>
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599 </data>
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600 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" >
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601 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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602 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
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603 <actions>
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604 <conditional name="output_format">
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605 <when value="rtable">
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606 <action type="format">
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607 <option type="from_param" name="output_format" />
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608 </action>
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609 </when>
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610 <when value="csv">
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611 <action type="format">
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612 <option type="from_param" name="output_format" />
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613 </action>
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614 </when>
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615 </conditional>
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616 </actions>
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617 </data>
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618 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" >
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619 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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620 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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621 <filter>'library' in partition_type</filter>
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622 <actions>
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623 <conditional name="output_format">
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624 <when value="rtable">
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625 <action type="format">
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626 <option type="from_param" name="output_format" />
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627 </action>
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628 </when>
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629 <when value="csv">
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630 <action type="format">
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631 <option type="from_param" name="output_format" />
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632 </action>
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633 </when>
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634 </conditional>
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635 </actions>
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636 </data>
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637 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" >
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638 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
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639 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
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640 <filter>'library' in partition_type</filter>
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641 <actions>
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642 <conditional name="output_format">
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643 <when value="rtable">
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644 <action type="format">
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645 <option type="from_param" name="output_format" />
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646 </action>
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647 </when>
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648 <when value="csv">
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649 <action type="format">
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650 <option type="from_param" name="output_format" />
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651 </action>
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652 </when>
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653 </conditional>
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654 </actions>
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655 </data>
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656
0
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657 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
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658 </outputs>
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659 <trackster_conf/>
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660 <tests>
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661 <test>
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662 <param name="reference_source_selector" value="history" />
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663 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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664 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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665 <param name="input_calculate_coverage_over_genes" />
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666 <param name="partition_type" value="sample" />
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667 <param name="summary_coverage_threshold_group" value="0" />
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668 <param name="output_format" value="rtable" />
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669 <param name="gatk_param_type_selector" value="basic" />
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670 <param name="analysis_param_type_selector" value="basic" />
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671 <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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672 <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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673 <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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674 <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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675 <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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676 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" />
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677 </test>
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678 </tests>
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parents:
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679 <help>
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parents:
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680 **What it does**
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681
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682 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.
0
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683
4
f244b8209eb8 bug fix release
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diff changeset
684 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_coverage_DepthOfCoverage.html&gt;`_.
0
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685
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686 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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687
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688 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
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689
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parents:
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690 ------
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691
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parents:
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692 **Inputs**
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693
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694 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.
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695
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696
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697 **Outputs**
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698
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699 The output is in various table formats.
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700
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701
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702 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
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703
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704 -------
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705
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706 **Settings**::
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707
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708 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
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709 ignoreDeletionSites boolean false Ignore sites consisting only of deletions
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710 includeDeletions boolean false Include information on deletions
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711 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
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712 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
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713 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
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714 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
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715 nBins int 499 Number of bins to use for granular binning
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716 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
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717 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
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718 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
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719 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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720 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
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721 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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722 printBaseCounts boolean false Will add base counts to per-locus output.
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723 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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724 start int 1 Starting (left endpoint) for granular binning
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725 stop int 500 Ending (right endpoint) for granular binning
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726 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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727
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728 @CITATION_SECTION@
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729 </help>
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730 <expand macro="citations" />
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731 </tool>