Mercurial > repos > iuc > gatk2
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 |
| rev | line source |
|---|---|
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1"> |
| 0 | 2 <description>on BAM files</description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
|
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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changeset
|
6 <expand macro="requirements" /> |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
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changeset
|
7 <expand macro="version_command" /> |
| 0 | 8 <command interpreter="python">gatk2_wrapper.py |
| 9 ##--max_jvm_heap_fraction "1" | |
| 10 --stdout "${output_log}" | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
11 @BAM_INPUTS@ |
| 0 | 12 -p ' |
| 13 @JAR_PATH@ | |
| 14 -T "DepthOfCoverage" | |
| 15 \$GATK2_SITE_OPTIONS | |
| 16 | |
| 17 @THREADS@ | |
| 18 | |
| 19 #if $reference_source.reference_source_selector != "history": | |
| 20 -R "${reference_source.ref_file.fields.path}" | |
| 21 #end if | |
| 22 #if str( $input_calculate_coverage_over_genes ) != "None": | |
| 23 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}" | |
| 24 #end if | |
| 25 #if str( $partition_type ) != "None": | |
| 26 #for $pt in str( $partition_type ).split( ',' ): | |
| 27 --partitionType "${pt}" | |
| 28 #end for | |
| 29 #end if | |
| 30 --out "${output_per_locus_coverage}" | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
31 |
| 0 | 32 #for $ct_group in $summary_coverage_threshold_group: |
| 33 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}" | |
| 34 #end for | |
| 35 --outputFormat "${output_format}" | |
| 36 ' | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
37 |
| 0 | 38 #include source=$standard_gatk_options# |
| 39 ##start analysis specific options | |
| 40 #if $analysis_param_type.analysis_param_type_selector == "advanced": | |
| 41 -p ' | |
| 42 ${analysis_param_type.ignore_deletion_sites} | |
| 43 ${analysis_param_type.include_deletions} | |
| 44 --maxBaseQuality "${analysis_param_type.max_base_quality}" | |
| 45 --maxMappingQuality "${analysis_param_type.max_mapping_quality}" | |
| 46 --minBaseQuality "${analysis_param_type.min_base_quality}" | |
| 47 --minMappingQuality "${analysis_param_type.min_mapping_quality}" | |
| 48 --nBins "${analysis_param_type.n_bins}" | |
| 49 ${analysis_param_type.omit_depth_output_at_each_base} | |
| 50 ${analysis_param_type.omit_interval_statistics} | |
| 51 ${analysis_param_type.omit_locus_table} | |
| 52 ${analysis_param_type.omit_per_sample_stats} | |
| 53 ${analysis_param_type.print_base_counts} | |
| 54 ${analysis_param_type.print_bin_endpoints_and_exit} | |
| 55 --start "${analysis_param_type.start}" | |
| 56 --stop "${analysis_param_type.stop}" | |
| 57 ' | |
| 58 #end if | |
| 59 ##Move additional files to final location | |
| 60 #if str( $partition_type ) != "None": | |
| 61 #set $partition_types = str( $partition_type ).split( ',' ) | |
| 62 #else: | |
| 63 #set $partition_types = [ 'sample' ] | |
| 64 #end if | |
| 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 ) == "" ): | |
| 66 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": | |
| 67 && mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample} | |
| 68 && mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample} | |
| 69 #end if | |
| 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 ) == "" ): | |
| 71 && mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample} | |
| 72 && mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample} | |
| 73 #end if | |
| 74 #if str( $input_calculate_coverage_over_genes ) != "None": | |
| 75 && mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample} | |
| 76 && mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample} | |
| 77 #end if | |
| 78 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": | |
| 79 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample} | |
| 80 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample} | |
| 81 #end if | |
| 82 #end if | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
83 |
| 0 | 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 ) == "" ): |
| 85 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": | |
| 86 && mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup} | |
| 87 && mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup} | |
| 88 #end if | |
| 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 ) == "" ): | |
| 90 && mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup} | |
| 91 && mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup} | |
| 92 #end if | |
| 93 #if str( $input_calculate_coverage_over_genes ) != "None": | |
| 94 && mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup} | |
| 95 && mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup} | |
| 96 #end if | |
| 97 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": | |
| 98 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup} | |
| 99 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup} | |
| 100 #end if | |
| 101 #end if | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
102 |
| 0 | 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 ) == "" ): |
| 104 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": | |
| 105 && mv ${output_per_locus_coverage}.library_summary ${output_summary_library} | |
| 106 && mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library} | |
| 107 #end if | |
| 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 ) == "" ): | |
| 109 && mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library} | |
| 110 && mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library} | |
| 111 #end if | |
| 112 #if str( $input_calculate_coverage_over_genes ) != "None": | |
| 113 && mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library} | |
| 114 && mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library} | |
| 115 #end if | |
| 116 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": | |
| 117 && mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library} | |
| 118 && mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library} | |
| 119 #end if | |
| 120 #end if | |
| 121 | |
| 122 </command> | |
| 123 <inputs> | |
| 124 <conditional name="reference_source"> | |
| 125 <expand macro="reference_source_selector_param" /> | |
| 126 <when value="cached"> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
127 <expand macro="input_bams_cached" /> |
| 0 | 128 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> |
| 129 <options from_data_table="gatk2_picard_indexes"> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
130 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> |
| 0 | 131 </options> |
| 132 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 133 </param> | |
| 134 </when> | |
| 135 <when value="history"> <!-- FIX ME!!!! --> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
136 |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
137 <expand macro="input_bams_history" /> |
| 0 | 138 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> |
| 139 </when> | |
| 140 </conditional> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
141 |
| 0 | 142 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &lt;calculateCoverageOverGenes&gt;" /> |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
143 |
| 0 | 144 <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &lt;partitionType&gt;"> |
| 145 <option value="sample" selected="True">sample</option> | |
| 146 <option value="readgroup">readgroup</option> | |
| 147 <option value="library">library</option> | |
| 148 </param> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
149 |
| 0 | 150 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &lt;summaryCoverageThreshold&gt;"> |
| 151 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to >= this number" /> | |
| 152 </repeat> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
153 |
| 0 | 154 <param name="output_format" type="select" label="Output format" help="--outputFormat &lt;outputFormat&gt;" > |
| 155 <option value="csv">csv</option> | |
| 156 <option value="table">table</option> | |
| 157 <option value="rtable" selected="True">rtable</option> | |
| 158 </param> | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
159 |
| 0 | 160 <expand macro="gatk_param_type_conditional" /> |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
161 |
| 0 | 162 <expand macro="analysis_type_conditional"> |
| 163 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" /> | |
| 164 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" /> | |
| 165 <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &lt;maxBaseQuality&gt;" /> | |
| 166 <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &lt;minBaseQuality&gt;" /> | |
| 167 <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &lt;maxMappingQuality&gt;" /> | |
| 168 <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality &lt;minMappingQuality&gt;" /> | |
| 169 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &lt;nBins&gt;" /> | |
| 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" /> | |
| 171 <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" /> | |
| 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" /> | |
| 173 <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" /> | |
| 174 <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" /> | |
| 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" /> | |
| 176 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &lt;start&gt;" /> | |
| 177 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &lt;stop&gt;" /> | |
| 178 </expand> | |
| 179 </inputs> | |
| 180 <outputs> | |
| 181 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" > | |
| 182 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 183 <actions> | |
| 184 <conditional name="output_format"> | |
| 185 <when value="rtable"> | |
| 186 <action type="format"> | |
| 187 <option type="from_param" name="output_format" /> | |
| 188 </action> | |
| 189 </when> | |
| 190 <when value="csv"> | |
| 191 <action type="format"> | |
| 192 <option type="from_param" name="output_format" /> | |
| 193 </action> | |
| 194 </when> | |
| 195 </conditional> | |
| 196 </actions> | |
| 197 </data> | |
| 198 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" > | |
| 199 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 200 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 201 <filter>'sample' in partition_type or not partition_type</filter> | |
| 202 <actions> | |
| 203 <conditional name="output_format"> | |
| 204 <when value="rtable"> | |
| 205 <action type="format"> | |
| 206 <option type="from_param" name="output_format" /> | |
| 207 </action> | |
| 208 </when> | |
| 209 <when value="csv"> | |
| 210 <action type="format"> | |
| 211 <option type="from_param" name="output_format" /> | |
| 212 </action> | |
| 213 </when> | |
| 214 </conditional> | |
| 215 </actions> | |
| 216 </data> | |
| 217 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" > | |
| 218 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 219 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 220 <filter>'sample' in partition_type or not partition_type</filter> | |
| 221 <actions> | |
| 222 <conditional name="output_format"> | |
| 223 <when value="rtable"> | |
| 224 <action type="format"> | |
| 225 <option type="from_param" name="output_format" /> | |
| 226 </action> | |
| 227 </when> | |
| 228 <when value="csv"> | |
| 229 <action type="format"> | |
| 230 <option type="from_param" name="output_format" /> | |
| 231 </action> | |
| 232 </when> | |
| 233 </conditional> | |
| 234 </actions> | |
| 235 </data> | |
| 236 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" > | |
| 237 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 238 <filter>'sample' in partition_type or not partition_type</filter> | |
| 239 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 240 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 241 <actions> | |
| 242 <conditional name="output_format"> | |
| 243 <when value="rtable"> | |
| 244 <action type="format"> | |
| 245 <option type="from_param" name="output_format" /> | |
| 246 </action> | |
| 247 </when> | |
| 248 <when value="csv"> | |
| 249 <action type="format"> | |
| 250 <option type="from_param" name="output_format" /> | |
| 251 </action> | |
| 252 </when> | |
| 253 </conditional> | |
| 254 </actions> | |
| 255 </data> | |
| 256 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" > | |
| 257 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 258 <filter>'sample' in partition_type or not partition_type</filter> | |
| 259 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 260 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 261 <actions> | |
| 262 <conditional name="output_format"> | |
| 263 <when value="rtable"> | |
| 264 <action type="format"> | |
| 265 <option type="from_param" name="output_format" /> | |
| 266 </action> | |
| 267 </when> | |
| 268 <when value="csv"> | |
| 269 <action type="format"> | |
| 270 <option type="from_param" name="output_format" /> | |
| 271 </action> | |
| 272 </when> | |
| 273 </conditional> | |
| 274 </actions> | |
| 275 </data> | |
| 276 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" > | |
| 277 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 278 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter> | |
| 279 <actions> | |
| 280 <conditional name="output_format"> | |
| 281 <when value="rtable"> | |
| 282 <action type="format"> | |
| 283 <option type="from_param" name="output_format" /> | |
| 284 </action> | |
| 285 </when> | |
| 286 <when value="csv"> | |
| 287 <action type="format"> | |
| 288 <option type="from_param" name="output_format" /> | |
| 289 </action> | |
| 290 </when> | |
| 291 </conditional> | |
| 292 </actions> | |
| 293 </data> | |
| 294 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" > | |
| 295 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 296 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter> | |
| 297 <actions> | |
| 298 <conditional name="output_format"> | |
| 299 <when value="rtable"> | |
| 300 <action type="format"> | |
| 301 <option type="from_param" name="output_format" /> | |
| 302 </action> | |
| 303 </when> | |
| 304 <when value="csv"> | |
| 305 <action type="format"> | |
| 306 <option type="from_param" name="output_format" /> | |
| 307 </action> | |
| 308 </when> | |
| 309 </conditional> | |
| 310 </actions> | |
| 311 </data> | |
| 312 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" > | |
| 313 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 314 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 315 <filter>'sample' in partition_type or not partition_type</filter> | |
| 316 <actions> | |
| 317 <conditional name="output_format"> | |
| 318 <when value="rtable"> | |
| 319 <action type="format"> | |
| 320 <option type="from_param" name="output_format" /> | |
| 321 </action> | |
| 322 </when> | |
| 323 <when value="csv"> | |
| 324 <action type="format"> | |
| 325 <option type="from_param" name="output_format" /> | |
| 326 </action> | |
| 327 </when> | |
| 328 </conditional> | |
| 329 </actions> | |
| 330 </data> | |
| 331 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" > | |
| 332 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 333 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 334 <filter>'sample' in partition_type or not partition_type</filter> | |
| 335 <actions> | |
| 336 <conditional name="output_format"> | |
| 337 <when value="rtable"> | |
| 338 <action type="format"> | |
| 339 <option type="from_param" name="output_format" /> | |
| 340 </action> | |
| 341 </when> | |
| 342 <when value="csv"> | |
| 343 <action type="format"> | |
| 344 <option type="from_param" name="output_format" /> | |
| 345 </action> | |
| 346 </when> | |
| 347 </conditional> | |
| 348 </actions> | |
| 349 </data> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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diff
changeset
|
350 |
| 0 | 351 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" > |
| 352 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 353 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 354 <filter>'readgroup' in partition_type</filter> | |
| 355 <actions> | |
| 356 <conditional name="output_format"> | |
| 357 <when value="rtable"> | |
| 358 <action type="format"> | |
| 359 <option type="from_param" name="output_format" /> | |
| 360 </action> | |
| 361 </when> | |
| 362 <when value="csv"> | |
| 363 <action type="format"> | |
| 364 <option type="from_param" name="output_format" /> | |
| 365 </action> | |
| 366 </when> | |
| 367 </conditional> | |
| 368 </actions> | |
| 369 </data> | |
| 370 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" > | |
| 371 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 372 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 373 <filter>'readgroup' in partition_type</filter> | |
| 374 <actions> | |
| 375 <conditional name="output_format"> | |
| 376 <when value="rtable"> | |
| 377 <action type="format"> | |
| 378 <option type="from_param" name="output_format" /> | |
| 379 </action> | |
| 380 </when> | |
| 381 <when value="csv"> | |
| 382 <action type="format"> | |
| 383 <option type="from_param" name="output_format" /> | |
| 384 </action> | |
| 385 </when> | |
| 386 </conditional> | |
| 387 </actions> | |
| 388 </data> | |
| 389 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" > | |
| 390 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 391 <filter>'readgroup' in partition_type</filter> | |
| 392 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 393 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 394 <actions> | |
| 395 <conditional name="output_format"> | |
| 396 <when value="rtable"> | |
| 397 <action type="format"> | |
| 398 <option type="from_param" name="output_format" /> | |
| 399 </action> | |
| 400 </when> | |
| 401 <when value="csv"> | |
| 402 <action type="format"> | |
| 403 <option type="from_param" name="output_format" /> | |
| 404 </action> | |
| 405 </when> | |
| 406 </conditional> | |
| 407 </actions> | |
| 408 </data> | |
| 409 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" > | |
| 410 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 411 <filter>'readgroup' in partition_type</filter> | |
| 412 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 413 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 414 <actions> | |
| 415 <conditional name="output_format"> | |
| 416 <when value="rtable"> | |
| 417 <action type="format"> | |
| 418 <option type="from_param" name="output_format" /> | |
| 419 </action> | |
| 420 </when> | |
| 421 <when value="csv"> | |
| 422 <action type="format"> | |
| 423 <option type="from_param" name="output_format" /> | |
| 424 </action> | |
| 425 </when> | |
| 426 </conditional> | |
| 427 </actions> | |
| 428 </data> | |
| 429 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" > | |
| 430 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 431 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter> | |
| 432 <actions> | |
| 433 <conditional name="output_format"> | |
| 434 <when value="rtable"> | |
| 435 <action type="format"> | |
| 436 <option type="from_param" name="output_format" /> | |
| 437 </action> | |
| 438 </when> | |
| 439 <when value="csv"> | |
| 440 <action type="format"> | |
| 441 <option type="from_param" name="output_format" /> | |
| 442 </action> | |
| 443 </when> | |
| 444 </conditional> | |
| 445 </actions> | |
| 446 </data> | |
| 447 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" > | |
| 448 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 449 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter> | |
| 450 <actions> | |
| 451 <conditional name="output_format"> | |
| 452 <when value="rtable"> | |
| 453 <action type="format"> | |
| 454 <option type="from_param" name="output_format" /> | |
| 455 </action> | |
| 456 </when> | |
| 457 <when value="csv"> | |
| 458 <action type="format"> | |
| 459 <option type="from_param" name="output_format" /> | |
| 460 </action> | |
| 461 </when> | |
| 462 </conditional> | |
| 463 </actions> | |
| 464 </data> | |
| 465 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" > | |
| 466 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 467 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 468 <filter>'readgroup' in partition_type</filter> | |
| 469 <actions> | |
| 470 <conditional name="output_format"> | |
| 471 <when value="rtable"> | |
| 472 <action type="format"> | |
| 473 <option type="from_param" name="output_format" /> | |
| 474 </action> | |
| 475 </when> | |
| 476 <when value="csv"> | |
| 477 <action type="format"> | |
| 478 <option type="from_param" name="output_format" /> | |
| 479 </action> | |
| 480 </when> | |
| 481 </conditional> | |
| 482 </actions> | |
| 483 </data> | |
| 484 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" > | |
| 485 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 486 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 487 <filter>'readgroup' in partition_type</filter> | |
| 488 <actions> | |
| 489 <conditional name="output_format"> | |
| 490 <when value="rtable"> | |
| 491 <action type="format"> | |
| 492 <option type="from_param" name="output_format" /> | |
| 493 </action> | |
| 494 </when> | |
| 495 <when value="csv"> | |
| 496 <action type="format"> | |
| 497 <option type="from_param" name="output_format" /> | |
| 498 </action> | |
| 499 </when> | |
| 500 </conditional> | |
| 501 </actions> | |
| 502 </data> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
503 |
| 0 | 504 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" > |
| 505 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 506 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 507 <filter>'library' in partition_type</filter> | |
| 508 <actions> | |
| 509 <conditional name="output_format"> | |
| 510 <when value="rtable"> | |
| 511 <action type="format"> | |
| 512 <option type="from_param" name="output_format" /> | |
| 513 </action> | |
| 514 </when> | |
| 515 <when value="csv"> | |
| 516 <action type="format"> | |
| 517 <option type="from_param" name="output_format" /> | |
| 518 </action> | |
| 519 </when> | |
| 520 </conditional> | |
| 521 </actions> | |
| 522 </data> | |
| 523 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" > | |
| 524 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 525 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 526 <filter>'library' in partition_type</filter> | |
| 527 <actions> | |
| 528 <conditional name="output_format"> | |
| 529 <when value="rtable"> | |
| 530 <action type="format"> | |
| 531 <option type="from_param" name="output_format" /> | |
| 532 </action> | |
| 533 </when> | |
| 534 <when value="csv"> | |
| 535 <action type="format"> | |
| 536 <option type="from_param" name="output_format" /> | |
| 537 </action> | |
| 538 </when> | |
| 539 </conditional> | |
| 540 </actions> | |
| 541 </data> | |
| 542 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" > | |
| 543 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 544 <filter>'library' in partition_type</filter> | |
| 545 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 546 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 547 <actions> | |
| 548 <conditional name="output_format"> | |
| 549 <when value="rtable"> | |
| 550 <action type="format"> | |
| 551 <option type="from_param" name="output_format" /> | |
| 552 </action> | |
| 553 </when> | |
| 554 <when value="csv"> | |
| 555 <action type="format"> | |
| 556 <option type="from_param" name="output_format" /> | |
| 557 </action> | |
| 558 </when> | |
| 559 </conditional> | |
| 560 </actions> | |
| 561 </data> | |
| 562 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" > | |
| 563 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 564 <filter>'library' in partition_type</filter> | |
| 565 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 566 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 567 <actions> | |
| 568 <conditional name="output_format"> | |
| 569 <when value="rtable"> | |
| 570 <action type="format"> | |
| 571 <option type="from_param" name="output_format" /> | |
| 572 </action> | |
| 573 </when> | |
| 574 <when value="csv"> | |
| 575 <action type="format"> | |
| 576 <option type="from_param" name="output_format" /> | |
| 577 </action> | |
| 578 </when> | |
| 579 </conditional> | |
| 580 </actions> | |
| 581 </data> | |
| 582 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" > | |
| 583 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 584 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter> | |
| 585 <actions> | |
| 586 <conditional name="output_format"> | |
| 587 <when value="rtable"> | |
| 588 <action type="format"> | |
| 589 <option type="from_param" name="output_format" /> | |
| 590 </action> | |
| 591 </when> | |
| 592 <when value="csv"> | |
| 593 <action type="format"> | |
| 594 <option type="from_param" name="output_format" /> | |
| 595 </action> | |
| 596 </when> | |
| 597 </conditional> | |
| 598 </actions> | |
| 599 </data> | |
| 600 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" > | |
| 601 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 602 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter> | |
| 603 <actions> | |
| 604 <conditional name="output_format"> | |
| 605 <when value="rtable"> | |
| 606 <action type="format"> | |
| 607 <option type="from_param" name="output_format" /> | |
| 608 </action> | |
| 609 </when> | |
| 610 <when value="csv"> | |
| 611 <action type="format"> | |
| 612 <option type="from_param" name="output_format" /> | |
| 613 </action> | |
| 614 </when> | |
| 615 </conditional> | |
| 616 </actions> | |
| 617 </data> | |
| 618 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" > | |
| 619 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 620 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 621 <filter>'library' in partition_type</filter> | |
| 622 <actions> | |
| 623 <conditional name="output_format"> | |
| 624 <when value="rtable"> | |
| 625 <action type="format"> | |
| 626 <option type="from_param" name="output_format" /> | |
| 627 </action> | |
| 628 </when> | |
| 629 <when value="csv"> | |
| 630 <action type="format"> | |
| 631 <option type="from_param" name="output_format" /> | |
| 632 </action> | |
| 633 </when> | |
| 634 </conditional> | |
| 635 </actions> | |
| 636 </data> | |
| 637 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" > | |
| 638 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 639 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 640 <filter>'library' in partition_type</filter> | |
| 641 <actions> | |
| 642 <conditional name="output_format"> | |
| 643 <when value="rtable"> | |
| 644 <action type="format"> | |
| 645 <option type="from_param" name="output_format" /> | |
| 646 </action> | |
| 647 </when> | |
| 648 <when value="csv"> | |
| 649 <action type="format"> | |
| 650 <option type="from_param" name="output_format" /> | |
| 651 </action> | |
| 652 </when> | |
| 653 </conditional> | |
| 654 </actions> | |
| 655 </data> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
656 |
| 0 | 657 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" /> |
| 658 </outputs> | |
| 659 <trackster_conf/> | |
| 660 <tests> | |
| 661 <test> | |
| 662 <param name="reference_source_selector" value="history" /> | |
| 663 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 664 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> | |
| 665 <param name="input_calculate_coverage_over_genes" /> | |
| 666 <param name="partition_type" value="sample" /> | |
| 667 <param name="summary_coverage_threshold_group" value="0" /> | |
| 668 <param name="output_format" value="rtable" /> | |
| 669 <param name="gatk_param_type_selector" value="basic" /> | |
| 670 <param name="analysis_param_type_selector" value="basic" /> | |
| 671 <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" /> | |
| 672 <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" /> | |
| 673 <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" /> | |
| 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" /> | |
| 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" /> | |
| 676 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" /> | |
| 677 </test> | |
| 678 </tests> | |
| 679 <help> | |
| 680 **What it does** | |
| 681 | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
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 | 683 |
| 4 | 684 For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html>`_. |
| 0 | 685 |
| 686 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 687 | |
| 688 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 689 | |
| 690 ------ | |
| 691 | |
| 692 **Inputs** | |
| 693 | |
| 694 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files. | |
| 695 | |
| 696 | |
| 697 **Outputs** | |
| 698 | |
| 699 The output is in various table formats. | |
| 700 | |
| 701 | |
| 702 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 703 | |
| 704 ------- | |
| 705 | |
| 706 **Settings**:: | |
| 707 | |
| 708 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. | |
| 709 ignoreDeletionSites boolean false Ignore sites consisting only of deletions | |
| 710 includeDeletions boolean false Include information on deletions | |
| 711 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). | |
| 712 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). | |
| 713 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. | |
| 714 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. | |
| 715 nBins int 499 Number of bins to use for granular binning | |
| 716 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup | |
| 717 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup | |
| 718 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup | |
| 719 omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. | |
| 720 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table | |
| 721 partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. | |
| 722 printBaseCounts boolean false Will add base counts to per-locus output. | |
| 723 printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. | |
| 724 start int 1 Starting (left endpoint) for granular binning | |
| 725 stop int 500 Ending (right endpoint) for granular binning | |
| 726 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. | |
| 727 | |
| 728 @CITATION_SECTION@ | |
| 729 </help> | |
| 4 | 730 <expand macro="citations" /> |
| 0 | 731 </tool> |