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comparison depth_of_coverage.xml @ 9:dcf1482b628c draft

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author lz_hust
date Sat, 01 Jun 2019 07:09:27 -0400
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8:3a8ef2ad0414 9:dcf1482b628c
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 &amp;&amp; mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
68 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
72 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
76 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
80 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
87 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
91 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
95 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
99 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
106 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
110 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
114 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
118 &amp;&amp; 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 &amp;lt;reference_sequence&amp;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 &amp;lt;reference_sequence&amp;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 &amp;lt;calculateCoverageOverGenes&amp;gt;" />
143
144 <param name="partition_type" type="select" label="Partition type for depth of coverage" multiple="True" display="checkboxes" help="-pt,--partitionType &amp;lt;partitionType&amp;gt;">
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 &amp;lt;summaryCoverageThreshold&amp;gt;">
151 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
152 </repeat>
153
154 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;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 &amp;lt;maxBaseQuality&amp;gt;" />
166 <param name="min_base_quality" type="integer" value="-1" label="Minimum quality of bases to count towards depth" help="-mbq,--minBaseQuality &amp;lt;minBaseQuality&amp;gt;" />
167 <param name="max_mapping_quality" type="integer" value="2147483647" label="Maximum mapping quality of reads to count towards depth." help="--maxMappingQuality &amp;lt;maxMappingQuality&amp;gt;" />
168 <param name="min_mapping_quality" type="integer" value="127" label="Minimum mapping quality of reads to count towards depth" help="-mmq,--minMappingQuality &amp;lt;minMappingQuality&amp;gt;" />
169 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &amp;lt;nBins&amp;gt;" />
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 &amp;lt;start&amp;gt;" />
177 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;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 &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html&gt;`_.
685
686 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
687
688 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
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 &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ 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>