|
9
|
1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.1">
|
|
|
2 <description>on BAM files</description>
|
|
|
3 <macros>
|
|
|
4 <import>gatk2_macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements" />
|
|
|
7 <expand macro="version_command" />
|
|
|
8 <command interpreter="python">gatk2_wrapper.py
|
|
|
9 ##--max_jvm_heap_fraction "1"
|
|
|
10 --stdout "${output_log}"
|
|
|
11 @BAM_INPUTS@
|
|
|
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}"
|
|
|
31
|
|
|
32 #for $ct_group in $summary_coverage_threshold_group:
|
|
|
33 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
|
|
|
34 #end for
|
|
|
35 --outputFormat "${output_format}"
|
|
|
36 '
|
|
|
37
|
|
|
38 #include source=$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
|
|
|
83
|
|
|
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
|
|
|
102
|
|
|
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">
|
|
|
127 <expand macro="input_bams_cached" />
|
|
|
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">
|
|
|
130 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
|
|
|
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!!!! -->
|
|
|
136
|
|
|
137 <expand macro="input_bams_history" />
|
|
|
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>
|
|
|
141
|
|
|
142 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &lt;calculateCoverageOverGenes&gt;" />
|
|
|
143
|
|
|
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>
|
|
|
149
|
|
|
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>
|
|
|
153
|
|
|
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>
|
|
|
159
|
|
|
160 <expand macro="gatk_param_type_conditional" />
|
|
|
161
|
|
|
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 ${on_string} (output cumulative coverage proportions sample)" >
|
|
|
332 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
|
|
|
333 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
334 <filter>'sample' in partition_type or not partition_type</filter>
|
|
|
335 <actions>
|
|
|
336 <conditional name="output_format">
|
|
|
337 <when value="rtable">
|
|
|
338 <action type="format">
|
|
|
339 <option type="from_param" name="output_format" />
|
|
|
340 </action>
|
|
|
341 </when>
|
|
|
342 <when value="csv">
|
|
|
343 <action type="format">
|
|
|
344 <option type="from_param" name="output_format" />
|
|
|
345 </action>
|
|
|
346 </when>
|
|
|
347 </conditional>
|
|
|
348 </actions>
|
|
|
349 </data>
|
|
|
350
|
|
|
351 <data format="tabular" name="output_summary_readgroup" label="${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 ${on_string} (output cumulative coverage proportions readgroup)" >
|
|
|
485 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
486 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
|
|
|
487 <filter>'readgroup' in partition_type</filter>
|
|
|
488 <actions>
|
|
|
489 <conditional name="output_format">
|
|
|
490 <when value="rtable">
|
|
|
491 <action type="format">
|
|
|
492 <option type="from_param" name="output_format" />
|
|
|
493 </action>
|
|
|
494 </when>
|
|
|
495 <when value="csv">
|
|
|
496 <action type="format">
|
|
|
497 <option type="from_param" name="output_format" />
|
|
|
498 </action>
|
|
|
499 </when>
|
|
|
500 </conditional>
|
|
|
501 </actions>
|
|
|
502 </data>
|
|
|
503
|
|
|
504 <data format="tabular" name="output_summary_library" label="${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 ${on_string} (output cumulative coverage proportions library)" >
|
|
|
638 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
|
|
|
639 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
|
|
|
640 <filter>'library' in partition_type</filter>
|
|
|
641 <actions>
|
|
|
642 <conditional name="output_format">
|
|
|
643 <when value="rtable">
|
|
|
644 <action type="format">
|
|
|
645 <option type="from_param" name="output_format" />
|
|
|
646 </action>
|
|
|
647 </when>
|
|
|
648 <when value="csv">
|
|
|
649 <action type="format">
|
|
|
650 <option type="from_param" name="output_format" />
|
|
|
651 </action>
|
|
|
652 </when>
|
|
|
653 </conditional>
|
|
|
654 </actions>
|
|
|
655 </data>
|
|
|
656
|
|
|
657 <data format="tabular" name="output_log" label="${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
|
|
|
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.
|
|
|
683
|
|
|
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>`_.
|
|
|
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>
|
|
|
730 <expand macro="citations" />
|
|
|
731 </tool>
|
