Mercurial > repos > iuc > gatk2
comparison depth_of_coverage.xml @ 0:340633249b3d draft
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author | bgruening |
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date | Mon, 02 Dec 2013 06:18:36 -0500 |
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children | f244b8209eb8 |
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-1:000000000000 | 0:340633249b3d |
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1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.7"> | |
2 <description>on BAM files</description> | |
3 <expand macro="requirements" /> | |
4 <macros> | |
5 <import>gatk2_macros.xml</import> | |
6 </macros> | |
7 <command interpreter="python">gatk2_wrapper.py | |
8 ##--max_jvm_heap_fraction "1" | |
9 --stdout "${output_log}" | |
10 #for $i, $input_bam in enumerate( $reference_source.input_bams ): | |
11 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}" | |
12 #if str( $input_bam.input_bam.metadata.bam_index ) != "None": | |
13 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index | |
14 #end if | |
15 #end for | |
16 -p ' | |
17 @JAR_PATH@ | |
18 -T "DepthOfCoverage" | |
19 \$GATK2_SITE_OPTIONS | |
20 | |
21 @THREADS@ | |
22 | |
23 #if $reference_source.reference_source_selector != "history": | |
24 -R "${reference_source.ref_file.fields.path}" | |
25 #end if | |
26 #if str( $input_calculate_coverage_over_genes ) != "None": | |
27 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}" | |
28 #end if | |
29 #if str( $partition_type ) != "None": | |
30 #for $pt in str( $partition_type ).split( ',' ): | |
31 --partitionType "${pt}" | |
32 #end for | |
33 #end if | |
34 --out "${output_per_locus_coverage}" | |
35 | |
36 #for $ct_group in $summary_coverage_threshold_group: | |
37 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}" | |
38 #end for | |
39 --outputFormat "${output_format}" | |
40 ' | |
41 | |
42 #include source=$standard_gatk_options# | |
43 ##start analysis specific options | |
44 #if $analysis_param_type.analysis_param_type_selector == "advanced": | |
45 -p ' | |
46 ${analysis_param_type.ignore_deletion_sites} | |
47 ${analysis_param_type.include_deletions} | |
48 --maxBaseQuality "${analysis_param_type.max_base_quality}" | |
49 --maxMappingQuality "${analysis_param_type.max_mapping_quality}" | |
50 --minBaseQuality "${analysis_param_type.min_base_quality}" | |
51 --minMappingQuality "${analysis_param_type.min_mapping_quality}" | |
52 --nBins "${analysis_param_type.n_bins}" | |
53 ${analysis_param_type.omit_depth_output_at_each_base} | |
54 ${analysis_param_type.omit_interval_statistics} | |
55 ${analysis_param_type.omit_locus_table} | |
56 ${analysis_param_type.omit_per_sample_stats} | |
57 ${analysis_param_type.print_base_counts} | |
58 ${analysis_param_type.print_bin_endpoints_and_exit} | |
59 --start "${analysis_param_type.start}" | |
60 --stop "${analysis_param_type.stop}" | |
61 ' | |
62 #end if | |
63 ##Move additional files to final location | |
64 #if str( $partition_type ) != "None": | |
65 #set $partition_types = str( $partition_type ).split( ',' ) | |
66 #else: | |
67 #set $partition_types = [ 'sample' ] | |
68 #end if | |
69 #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 ) == "" ): | |
70 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": | |
71 && mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample} | |
72 && mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample} | |
73 #end if | |
74 #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 ) == "" ): | |
75 && mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample} | |
76 && mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample} | |
77 #end if | |
78 #if str( $input_calculate_coverage_over_genes ) != "None": | |
79 && mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample} | |
80 && mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample} | |
81 #end if | |
82 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": | |
83 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample} | |
84 && mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample} | |
85 #end if | |
86 #end if | |
87 | |
88 #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 ) == "" ): | |
89 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": | |
90 && mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup} | |
91 && mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup} | |
92 #end if | |
93 #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 ) == "" ): | |
94 && mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup} | |
95 && mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup} | |
96 #end if | |
97 #if str( $input_calculate_coverage_over_genes ) != "None": | |
98 && mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup} | |
99 && mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup} | |
100 #end if | |
101 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": | |
102 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup} | |
103 && mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup} | |
104 #end if | |
105 #end if | |
106 | |
107 #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 ) == "" ): | |
108 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "": | |
109 && mv ${output_per_locus_coverage}.library_summary ${output_summary_library} | |
110 && mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library} | |
111 #end if | |
112 #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 ) == "" ): | |
113 && mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library} | |
114 && mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library} | |
115 #end if | |
116 #if str( $input_calculate_coverage_over_genes ) != "None": | |
117 && mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library} | |
118 && mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library} | |
119 #end if | |
120 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "": | |
121 && mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library} | |
122 && mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library} | |
123 #end if | |
124 #end if | |
125 | |
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"> | |
140 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> | |
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> | |
152 | |
153 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &lt;calculateCoverageOverGenes&gt;" /> | |
154 | |
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> | |
160 | |
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> | |
164 | |
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> | |
170 | |
171 <expand macro="gatk_param_type_conditional" /> | |
172 | |
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 ${on_string} (output cumulative coverage proportions sample)" > | |
343 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
344 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
345 <filter>'sample' in partition_type or not partition_type</filter> | |
346 <actions> | |
347 <conditional name="output_format"> | |
348 <when value="rtable"> | |
349 <action type="format"> | |
350 <option type="from_param" name="output_format" /> | |
351 </action> | |
352 </when> | |
353 <when value="csv"> | |
354 <action type="format"> | |
355 <option type="from_param" name="output_format" /> | |
356 </action> | |
357 </when> | |
358 </conditional> | |
359 </actions> | |
360 </data> | |
361 | |
362 <data format="tabular" name="output_summary_readgroup" label="${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 ${on_string} (output cumulative coverage proportions readgroup)" > | |
496 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
497 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
498 <filter>'readgroup' in partition_type</filter> | |
499 <actions> | |
500 <conditional name="output_format"> | |
501 <when value="rtable"> | |
502 <action type="format"> | |
503 <option type="from_param" name="output_format" /> | |
504 </action> | |
505 </when> | |
506 <when value="csv"> | |
507 <action type="format"> | |
508 <option type="from_param" name="output_format" /> | |
509 </action> | |
510 </when> | |
511 </conditional> | |
512 </actions> | |
513 </data> | |
514 | |
515 <data format="tabular" name="output_summary_library" label="${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 ${on_string} (output cumulative coverage proportions library)" > | |
649 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter> | |
650 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter> | |
651 <filter>'library' in partition_type</filter> | |
652 <actions> | |
653 <conditional name="output_format"> | |
654 <when value="rtable"> | |
655 <action type="format"> | |
656 <option type="from_param" name="output_format" /> | |
657 </action> | |
658 </when> | |
659 <when value="csv"> | |
660 <action type="format"> | |
661 <option type="from_param" name="output_format" /> | |
662 </action> | |
663 </when> | |
664 </conditional> | |
665 </actions> | |
666 </data> | |
667 | |
668 <data format="tabular" name="output_log" label="${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 | |
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. | |
694 | |
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_annotator_DepthOfCoverage.html>`_. | |
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> | |
741 </tool> |