Mercurial > repos > iuc > gatk2
annotate depth_of_coverage.xml @ 11:0d369d08ad6e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
| author | iuc |
|---|---|
| date | Mon, 04 May 2015 22:47:06 -0400 |
| parents | b80301676614 |
| children | 669a23f1f4b5 |
| rev | line source |
|---|---|
| 6 | 1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0"> |
| 0 | 2 <description>on BAM files</description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
|
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0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
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changeset
|
6 <expand macro="requirements" /> |
|
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
7 <expand macro="version_command" /> |
| 0 | 8 <command interpreter="python">gatk2_wrapper.py |
| 9 ##--max_jvm_heap_fraction "1" | |
| 10 --stdout "${output_log}" | |
| 11 #for $i, $input_bam in enumerate( $reference_source.input_bams ): | |
| 12 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" | |
| 13 #if str( $input_bam.input_bam.metadata.bam_index ) != "None": | |
| 14 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index | |
| 15 #end if | |
| 16 #end for | |
| 17 -p ' | |
| 18 @JAR_PATH@ | |
| 19 -T "DepthOfCoverage" | |
| 20 \$GATK2_SITE_OPTIONS | |
| 21 | |
| 22 @THREADS@ | |
| 23 | |
| 24 #if $reference_source.reference_source_selector != "history": | |
| 25 -R "${reference_source.ref_file.fields.path}" | |
| 26 #end if | |
| 27 #if str( $input_calculate_coverage_over_genes ) != "None": | |
| 28 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}" | |
| 29 #end if | |
| 30 #if str( $partition_type ) != "None": | |
| 31 #for $pt in str( $partition_type ).split( ',' ): | |
| 32 --partitionType "${pt}" | |
| 33 #end for | |
| 34 #end if | |
| 35 --out "${output_per_locus_coverage}" | |
|
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0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
36 |
| 0 | 37 #for $ct_group in $summary_coverage_threshold_group: |
| 38 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}" | |
| 39 #end for | |
| 40 --outputFormat "${output_format}" | |
| 41 ' | |
|
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0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
42 |
| 0 | 43 #include source=$standard_gatk_options# |
| 44 ##start analysis specific options | |
| 45 #if $analysis_param_type.analysis_param_type_selector == "advanced": | |
| 46 -p ' | |
| 47 ${analysis_param_type.ignore_deletion_sites} | |
| 48 ${analysis_param_type.include_deletions} | |
| 49 --maxBaseQuality "${analysis_param_type.max_base_quality}" | |
| 50 --maxMappingQuality "${analysis_param_type.max_mapping_quality}" | |
| 51 --minBaseQuality "${analysis_param_type.min_base_quality}" | |
| 52 --minMappingQuality "${analysis_param_type.min_mapping_quality}" | |
| 53 --nBins "${analysis_param_type.n_bins}" | |
| 54 ${analysis_param_type.omit_depth_output_at_each_base} | |
| 55 ${analysis_param_type.omit_interval_statistics} | |
| 56 ${analysis_param_type.omit_locus_table} | |
| 57 ${analysis_param_type.omit_per_sample_stats} | |
| 58 ${analysis_param_type.print_base_counts} | |
| 59 ${analysis_param_type.print_bin_endpoints_and_exit} | |
| 60 --start "${analysis_param_type.start}" | |
| 61 --stop "${analysis_param_type.stop}" | |
| 62 ' | |
| 63 #end if | |
| 64 ##Move additional files to final location | |
| 65 #if str( $partition_type ) != "None": | |
| 66 #set $partition_types = str( $partition_type ).split( ',' ) | |
| 67 #else: | |
| 68 #set $partition_types = [ 'sample' ] | |
| 69 #end if | |
| 70 #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 ) == "" ): | |
| 71 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": | |
| 72 && mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample} | |
| 73 && mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample} | |
| 74 #end if | |
| 75 #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 ) == "" ): | |
| 76 && mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample} | |
| 77 && mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample} | |
| 78 #end if | |
| 79 #if str( $input_calculate_coverage_over_genes ) != "None": | |
| 80 && mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample} | |
| 81 && mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample} | |
| 82 #end if | |
| 83 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": | |
| 84 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample} | |
| 85 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample} | |
| 86 #end if | |
| 87 #end if | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
88 |
| 0 | 89 #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 ) == "" ): |
| 90 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": | |
| 91 && mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup} | |
| 92 && mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup} | |
| 93 #end if | |
| 94 #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 ) == "" ): | |
| 95 && mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup} | |
| 96 && mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup} | |
| 97 #end if | |
| 98 #if str( $input_calculate_coverage_over_genes ) != "None": | |
| 99 && mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup} | |
| 100 && mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup} | |
| 101 #end if | |
| 102 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": | |
| 103 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup} | |
| 104 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup} | |
| 105 #end if | |
| 106 #end if | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
107 |
| 0 | 108 #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 ) == "" ): |
| 109 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": | |
| 110 && mv ${output_per_locus_coverage}.library_summary ${output_summary_library} | |
| 111 && mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library} | |
| 112 #end if | |
| 113 #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 ) == "" ): | |
| 114 && mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library} | |
| 115 && mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library} | |
| 116 #end if | |
| 117 #if str( $input_calculate_coverage_over_genes ) != "None": | |
| 118 && mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library} | |
| 119 && mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library} | |
| 120 #end if | |
| 121 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": | |
| 122 && mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library} | |
| 123 && mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library} | |
| 124 #end if | |
| 125 #end if | |
| 126 | |
| 127 </command> | |
| 128 <inputs> | |
| 129 <conditional name="reference_source"> | |
| 130 <expand macro="reference_source_selector_param" /> | |
| 131 <when value="cached"> | |
| 132 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> | |
| 133 <param name="input_bam" type="data" format="bam" label="BAM file"> | |
| 134 <validator type="unspecified_build" /> | |
| 135 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select --> | |
| 136 </param> | |
| 137 </repeat> | |
| 138 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> | |
| 139 <options from_data_table="gatk2_picard_indexes"> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
140 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> |
| 0 | 141 </options> |
| 142 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 143 </param> | |
| 144 </when> | |
| 145 <when value="history"> <!-- FIX ME!!!! --> | |
| 146 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &lt;input_file&gt;"> | |
| 147 <param name="input_bam" type="data" format="bam" label="BAM file" /> | |
| 148 </repeat> | |
| 149 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> | |
| 150 </when> | |
| 151 </conditional> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
152 |
| 0 | 153 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &lt;calculateCoverageOverGenes&gt;" /> |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
154 |
| 0 | 155 <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &lt;partitionType&gt;"> |
| 156 <option value="sample" selected="True">sample</option> | |
| 157 <option value="readgroup">readgroup</option> | |
| 158 <option value="library">library</option> | |
| 159 </param> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
160 |
| 0 | 161 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &lt;summaryCoverageThreshold&gt;"> |
| 162 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to >= this number" /> | |
| 163 </repeat> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
164 |
| 0 | 165 <param name="output_format" type="select" label="Output format" help="--outputFormat &lt;outputFormat&gt;" > |
| 166 <option value="csv">csv</option> | |
| 167 <option value="table">table</option> | |
| 168 <option value="rtable" selected="True">rtable</option> | |
| 169 </param> | |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
170 |
| 0 | 171 <expand macro="gatk_param_type_conditional" /> |
|
11
0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
172 |
| 0 | 173 <expand macro="analysis_type_conditional"> |
| 174 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" /> | |
| 175 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" /> | |
| 176 <param name="max_base_quality" type="integer" value="127" label="Maximum quality of bases to count towards depth" help="--maxBaseQuality &lt;maxBaseQuality&gt;" /> | |
| 177 <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &lt;minBaseQuality&gt;" /> | |
| 178 <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &lt;maxMappingQuality&gt;" /> | |
| 179 <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality &lt;minMappingQuality&gt;" /> | |
| 180 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &lt;nBins&gt;" /> | |
| 181 <param name="omit_depth_output_at_each_base" type="boolean" truevalue="--omitDepthOutputAtEachBase" falsevalue="" checked="False" label="Omit the output of the depth of coverage at each base" help="-omitBaseOutput,--omitDepthOutputAtEachBase" /> | |
| 182 <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" /> | |
| 183 <param name="omit_locus_table" type="boolean" truevalue="--omitLocusTable" falsevalue="" checked="False" label="Do not calculate the per-sample per-depth counts of loci" help="-omitLocusTable,--omitLocusTable" /> | |
| 184 <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" /> | |
| 185 <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" /> | |
| 186 <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" /> | |
| 187 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &lt;start&gt;" /> | |
| 188 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &lt;stop&gt;" /> | |
| 189 </expand> | |
| 190 </inputs> | |
| 191 <outputs> | |
| 192 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" > | |
| 193 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 194 <actions> | |
| 195 <conditional name="output_format"> | |
| 196 <when value="rtable"> | |
| 197 <action type="format"> | |
| 198 <option type="from_param" name="output_format" /> | |
| 199 </action> | |
| 200 </when> | |
| 201 <when value="csv"> | |
| 202 <action type="format"> | |
| 203 <option type="from_param" name="output_format" /> | |
| 204 </action> | |
| 205 </when> | |
| 206 </conditional> | |
| 207 </actions> | |
| 208 </data> | |
| 209 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" > | |
| 210 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 211 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 212 <filter>'sample' in partition_type or not partition_type</filter> | |
| 213 <actions> | |
| 214 <conditional name="output_format"> | |
| 215 <when value="rtable"> | |
| 216 <action type="format"> | |
| 217 <option type="from_param" name="output_format" /> | |
| 218 </action> | |
| 219 </when> | |
| 220 <when value="csv"> | |
| 221 <action type="format"> | |
| 222 <option type="from_param" name="output_format" /> | |
| 223 </action> | |
| 224 </when> | |
| 225 </conditional> | |
| 226 </actions> | |
| 227 </data> | |
| 228 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" > | |
| 229 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 230 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 231 <filter>'sample' in partition_type or not partition_type</filter> | |
| 232 <actions> | |
| 233 <conditional name="output_format"> | |
| 234 <when value="rtable"> | |
| 235 <action type="format"> | |
| 236 <option type="from_param" name="output_format" /> | |
| 237 </action> | |
| 238 </when> | |
| 239 <when value="csv"> | |
| 240 <action type="format"> | |
| 241 <option type="from_param" name="output_format" /> | |
| 242 </action> | |
| 243 </when> | |
| 244 </conditional> | |
| 245 </actions> | |
| 246 </data> | |
| 247 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" > | |
| 248 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 249 <filter>'sample' in partition_type or not partition_type</filter> | |
| 250 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 251 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 252 <actions> | |
| 253 <conditional name="output_format"> | |
| 254 <when value="rtable"> | |
| 255 <action type="format"> | |
| 256 <option type="from_param" name="output_format" /> | |
| 257 </action> | |
| 258 </when> | |
| 259 <when value="csv"> | |
| 260 <action type="format"> | |
| 261 <option type="from_param" name="output_format" /> | |
| 262 </action> | |
| 263 </when> | |
| 264 </conditional> | |
| 265 </actions> | |
| 266 </data> | |
| 267 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" > | |
| 268 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 269 <filter>'sample' in partition_type or not partition_type</filter> | |
| 270 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 271 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 272 <actions> | |
| 273 <conditional name="output_format"> | |
| 274 <when value="rtable"> | |
| 275 <action type="format"> | |
| 276 <option type="from_param" name="output_format" /> | |
| 277 </action> | |
| 278 </when> | |
| 279 <when value="csv"> | |
| 280 <action type="format"> | |
| 281 <option type="from_param" name="output_format" /> | |
| 282 </action> | |
| 283 </when> | |
| 284 </conditional> | |
| 285 </actions> | |
| 286 </data> | |
| 287 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" > | |
| 288 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 289 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter> | |
| 290 <actions> | |
| 291 <conditional name="output_format"> | |
| 292 <when value="rtable"> | |
| 293 <action type="format"> | |
| 294 <option type="from_param" name="output_format" /> | |
| 295 </action> | |
| 296 </when> | |
| 297 <when value="csv"> | |
| 298 <action type="format"> | |
| 299 <option type="from_param" name="output_format" /> | |
| 300 </action> | |
| 301 </when> | |
| 302 </conditional> | |
| 303 </actions> | |
| 304 </data> | |
| 305 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" > | |
| 306 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 307 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter> | |
| 308 <actions> | |
| 309 <conditional name="output_format"> | |
| 310 <when value="rtable"> | |
| 311 <action type="format"> | |
| 312 <option type="from_param" name="output_format" /> | |
| 313 </action> | |
| 314 </when> | |
| 315 <when value="csv"> | |
| 316 <action type="format"> | |
| 317 <option type="from_param" name="output_format" /> | |
| 318 </action> | |
| 319 </when> | |
| 320 </conditional> | |
| 321 </actions> | |
| 322 </data> | |
| 323 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" > | |
| 324 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 325 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 326 <filter>'sample' in partition_type or not partition_type</filter> | |
| 327 <actions> | |
| 328 <conditional name="output_format"> | |
| 329 <when value="rtable"> | |
| 330 <action type="format"> | |
| 331 <option type="from_param" name="output_format" /> | |
| 332 </action> | |
| 333 </when> | |
| 334 <when value="csv"> | |
| 335 <action type="format"> | |
| 336 <option type="from_param" name="output_format" /> | |
| 337 </action> | |
| 338 </when> | |
| 339 </conditional> | |
| 340 </actions> | |
| 341 </data> | |
| 342 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" > | |
| 343 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 344 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 345 <filter>'sample' in partition_type or not partition_type</filter> | |
| 346 <actions> | |
| 347 <conditional name="output_format"> | |
| 348 <when value="rtable"> | |
| 349 <action type="format"> | |
| 350 <option type="from_param" name="output_format" /> | |
| 351 </action> | |
| 352 </when> | |
| 353 <when value="csv"> | |
| 354 <action type="format"> | |
| 355 <option type="from_param" name="output_format" /> | |
| 356 </action> | |
| 357 </when> | |
| 358 </conditional> | |
| 359 </actions> | |
| 360 </data> | |
|
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0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
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diff
changeset
|
361 |
| 0 | 362 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" > |
| 363 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 364 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 365 <filter>'readgroup' in partition_type</filter> | |
| 366 <actions> | |
| 367 <conditional name="output_format"> | |
| 368 <when value="rtable"> | |
| 369 <action type="format"> | |
| 370 <option type="from_param" name="output_format" /> | |
| 371 </action> | |
| 372 </when> | |
| 373 <when value="csv"> | |
| 374 <action type="format"> | |
| 375 <option type="from_param" name="output_format" /> | |
| 376 </action> | |
| 377 </when> | |
| 378 </conditional> | |
| 379 </actions> | |
| 380 </data> | |
| 381 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" > | |
| 382 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 383 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 384 <filter>'readgroup' in partition_type</filter> | |
| 385 <actions> | |
| 386 <conditional name="output_format"> | |
| 387 <when value="rtable"> | |
| 388 <action type="format"> | |
| 389 <option type="from_param" name="output_format" /> | |
| 390 </action> | |
| 391 </when> | |
| 392 <when value="csv"> | |
| 393 <action type="format"> | |
| 394 <option type="from_param" name="output_format" /> | |
| 395 </action> | |
| 396 </when> | |
| 397 </conditional> | |
| 398 </actions> | |
| 399 </data> | |
| 400 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" > | |
| 401 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 402 <filter>'readgroup' in partition_type</filter> | |
| 403 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 404 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 405 <actions> | |
| 406 <conditional name="output_format"> | |
| 407 <when value="rtable"> | |
| 408 <action type="format"> | |
| 409 <option type="from_param" name="output_format" /> | |
| 410 </action> | |
| 411 </when> | |
| 412 <when value="csv"> | |
| 413 <action type="format"> | |
| 414 <option type="from_param" name="output_format" /> | |
| 415 </action> | |
| 416 </when> | |
| 417 </conditional> | |
| 418 </actions> | |
| 419 </data> | |
| 420 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" > | |
| 421 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 422 <filter>'readgroup' in partition_type</filter> | |
| 423 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 424 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 425 <actions> | |
| 426 <conditional name="output_format"> | |
| 427 <when value="rtable"> | |
| 428 <action type="format"> | |
| 429 <option type="from_param" name="output_format" /> | |
| 430 </action> | |
| 431 </when> | |
| 432 <when value="csv"> | |
| 433 <action type="format"> | |
| 434 <option type="from_param" name="output_format" /> | |
| 435 </action> | |
| 436 </when> | |
| 437 </conditional> | |
| 438 </actions> | |
| 439 </data> | |
| 440 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" > | |
| 441 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 442 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter> | |
| 443 <actions> | |
| 444 <conditional name="output_format"> | |
| 445 <when value="rtable"> | |
| 446 <action type="format"> | |
| 447 <option type="from_param" name="output_format" /> | |
| 448 </action> | |
| 449 </when> | |
| 450 <when value="csv"> | |
| 451 <action type="format"> | |
| 452 <option type="from_param" name="output_format" /> | |
| 453 </action> | |
| 454 </when> | |
| 455 </conditional> | |
| 456 </actions> | |
| 457 </data> | |
| 458 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" > | |
| 459 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 460 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter> | |
| 461 <actions> | |
| 462 <conditional name="output_format"> | |
| 463 <when value="rtable"> | |
| 464 <action type="format"> | |
| 465 <option type="from_param" name="output_format" /> | |
| 466 </action> | |
| 467 </when> | |
| 468 <when value="csv"> | |
| 469 <action type="format"> | |
| 470 <option type="from_param" name="output_format" /> | |
| 471 </action> | |
| 472 </when> | |
| 473 </conditional> | |
| 474 </actions> | |
| 475 </data> | |
| 476 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" > | |
| 477 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 478 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 479 <filter>'readgroup' in partition_type</filter> | |
| 480 <actions> | |
| 481 <conditional name="output_format"> | |
| 482 <when value="rtable"> | |
| 483 <action type="format"> | |
| 484 <option type="from_param" name="output_format" /> | |
| 485 </action> | |
| 486 </when> | |
| 487 <when value="csv"> | |
| 488 <action type="format"> | |
| 489 <option type="from_param" name="output_format" /> | |
| 490 </action> | |
| 491 </when> | |
| 492 </conditional> | |
| 493 </actions> | |
| 494 </data> | |
| 495 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" > | |
| 496 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 497 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 498 <filter>'readgroup' in partition_type</filter> | |
| 499 <actions> | |
| 500 <conditional name="output_format"> | |
| 501 <when value="rtable"> | |
| 502 <action type="format"> | |
| 503 <option type="from_param" name="output_format" /> | |
| 504 </action> | |
| 505 </when> | |
| 506 <when value="csv"> | |
| 507 <action type="format"> | |
| 508 <option type="from_param" name="output_format" /> | |
| 509 </action> | |
| 510 </when> | |
| 511 </conditional> | |
| 512 </actions> | |
| 513 </data> | |
|
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0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
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diff
changeset
|
514 |
| 0 | 515 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" > |
| 516 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 517 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 518 <filter>'library' in partition_type</filter> | |
| 519 <actions> | |
| 520 <conditional name="output_format"> | |
| 521 <when value="rtable"> | |
| 522 <action type="format"> | |
| 523 <option type="from_param" name="output_format" /> | |
| 524 </action> | |
| 525 </when> | |
| 526 <when value="csv"> | |
| 527 <action type="format"> | |
| 528 <option type="from_param" name="output_format" /> | |
| 529 </action> | |
| 530 </when> | |
| 531 </conditional> | |
| 532 </actions> | |
| 533 </data> | |
| 534 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" > | |
| 535 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter> | |
| 536 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 537 <filter>'library' in partition_type</filter> | |
| 538 <actions> | |
| 539 <conditional name="output_format"> | |
| 540 <when value="rtable"> | |
| 541 <action type="format"> | |
| 542 <option type="from_param" name="output_format" /> | |
| 543 </action> | |
| 544 </when> | |
| 545 <when value="csv"> | |
| 546 <action type="format"> | |
| 547 <option type="from_param" name="output_format" /> | |
| 548 </action> | |
| 549 </when> | |
| 550 </conditional> | |
| 551 </actions> | |
| 552 </data> | |
| 553 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" > | |
| 554 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 555 <filter>'library' in partition_type</filter> | |
| 556 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 557 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 558 <actions> | |
| 559 <conditional name="output_format"> | |
| 560 <when value="rtable"> | |
| 561 <action type="format"> | |
| 562 <option type="from_param" name="output_format" /> | |
| 563 </action> | |
| 564 </when> | |
| 565 <when value="csv"> | |
| 566 <action type="format"> | |
| 567 <option type="from_param" name="output_format" /> | |
| 568 </action> | |
| 569 </when> | |
| 570 </conditional> | |
| 571 </actions> | |
| 572 </data> | |
| 573 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" > | |
| 574 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 575 <filter>'library' in partition_type</filter> | |
| 576 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter> | |
| 577 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter> | |
| 578 <actions> | |
| 579 <conditional name="output_format"> | |
| 580 <when value="rtable"> | |
| 581 <action type="format"> | |
| 582 <option type="from_param" name="output_format" /> | |
| 583 </action> | |
| 584 </when> | |
| 585 <when value="csv"> | |
| 586 <action type="format"> | |
| 587 <option type="from_param" name="output_format" /> | |
| 588 </action> | |
| 589 </when> | |
| 590 </conditional> | |
| 591 </actions> | |
| 592 </data> | |
| 593 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" > | |
| 594 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 595 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter> | |
| 596 <actions> | |
| 597 <conditional name="output_format"> | |
| 598 <when value="rtable"> | |
| 599 <action type="format"> | |
| 600 <option type="from_param" name="output_format" /> | |
| 601 </action> | |
| 602 </when> | |
| 603 <when value="csv"> | |
| 604 <action type="format"> | |
| 605 <option type="from_param" name="output_format" /> | |
| 606 </action> | |
| 607 </when> | |
| 608 </conditional> | |
| 609 </actions> | |
| 610 </data> | |
| 611 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" > | |
| 612 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 613 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter> | |
| 614 <actions> | |
| 615 <conditional name="output_format"> | |
| 616 <when value="rtable"> | |
| 617 <action type="format"> | |
| 618 <option type="from_param" name="output_format" /> | |
| 619 </action> | |
| 620 </when> | |
| 621 <when value="csv"> | |
| 622 <action type="format"> | |
| 623 <option type="from_param" name="output_format" /> | |
| 624 </action> | |
| 625 </when> | |
| 626 </conditional> | |
| 627 </actions> | |
| 628 </data> | |
| 629 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" > | |
| 630 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 631 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 632 <filter>'library' in partition_type</filter> | |
| 633 <actions> | |
| 634 <conditional name="output_format"> | |
| 635 <when value="rtable"> | |
| 636 <action type="format"> | |
| 637 <option type="from_param" name="output_format" /> | |
| 638 </action> | |
| 639 </when> | |
| 640 <when value="csv"> | |
| 641 <action type="format"> | |
| 642 <option type="from_param" name="output_format" /> | |
| 643 </action> | |
| 644 </when> | |
| 645 </conditional> | |
| 646 </actions> | |
| 647 </data> | |
| 648 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" > | |
| 649 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
| 650 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
| 651 <filter>'library' in partition_type</filter> | |
| 652 <actions> | |
| 653 <conditional name="output_format"> | |
| 654 <when value="rtable"> | |
| 655 <action type="format"> | |
| 656 <option type="from_param" name="output_format" /> | |
| 657 </action> | |
| 658 </when> | |
| 659 <when value="csv"> | |
| 660 <action type="format"> | |
| 661 <option type="from_param" name="output_format" /> | |
| 662 </action> | |
| 663 </when> | |
| 664 </conditional> | |
| 665 </actions> | |
| 666 </data> | |
|
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0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
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diff
changeset
|
667 |
| 0 | 668 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" /> |
| 669 </outputs> | |
| 670 <trackster_conf/> | |
| 671 <tests> | |
| 672 <test> | |
| 673 <param name="reference_source_selector" value="history" /> | |
| 674 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 675 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> | |
| 676 <param name="input_calculate_coverage_over_genes" /> | |
| 677 <param name="partition_type" value="sample" /> | |
| 678 <param name="summary_coverage_threshold_group" value="0" /> | |
| 679 <param name="output_format" value="rtable" /> | |
| 680 <param name="gatk_param_type_selector" value="basic" /> | |
| 681 <param name="analysis_param_type_selector" value="basic" /> | |
| 682 <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" /> | |
| 683 <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" /> | |
| 684 <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" /> | |
| 685 <output name="output_cumulative_coverage_counts_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_cumulative_coverage_counts_sample.tabular" /> | |
| 686 <output name="output_cumulative_coverage_proportions_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_output_cumulative_coverage_proportions_sample.tabular" /> | |
| 687 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" /> | |
| 688 </test> | |
| 689 </tests> | |
| 690 <help> | |
| 691 **What it does** | |
| 692 | |
|
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0d369d08ad6e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
6
diff
changeset
|
693 DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score. |
| 0 | 694 |
| 6 | 695 For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html>`_. |
| 0 | 696 |
| 697 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 698 | |
| 699 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 700 | |
| 701 ------ | |
| 702 | |
| 703 **Inputs** | |
| 704 | |
| 705 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files. | |
| 706 | |
| 707 | |
| 708 **Outputs** | |
| 709 | |
| 710 The output is in various table formats. | |
| 711 | |
| 712 | |
| 713 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 714 | |
| 715 ------- | |
| 716 | |
| 717 **Settings**:: | |
| 718 | |
| 719 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq. | |
| 720 ignoreDeletionSites boolean false Ignore sites consisting only of deletions | |
| 721 includeDeletions boolean false Include information on deletions | |
| 722 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE). | |
| 723 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE). | |
| 724 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1. | |
| 725 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1. | |
| 726 nBins int 499 Number of bins to use for granular binning | |
| 727 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup | |
| 728 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup | |
| 729 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup | |
| 730 omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime. | |
| 731 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table | |
| 732 partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library. | |
| 733 printBaseCounts boolean false Will add base counts to per-locus output. | |
| 734 printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data. | |
| 735 start int 1 Starting (left endpoint) for granular binning | |
| 736 stop int 500 Ending (right endpoint) for granular binning | |
| 737 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. | |
| 738 | |
| 739 @CITATION_SECTION@ | |
| 740 </help> | |
| 6 | 741 <expand macro="citations" /> |
| 0 | 742 </tool> |