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comparison depth_of_coverage.xml @ 0:340633249b3d draft

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author bgruening
date Mon, 02 Dec 2013 06:18:36 -0500
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-1:000000000000 0:340633249b3d
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 &amp;&amp; mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
72 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
76 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
80 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
84 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
91 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
95 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
99 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
103 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
110 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
114 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
118 &amp;&amp; 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 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
122 &amp;&amp; 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 &amp;lt;input_file&amp;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 &amp;lt;reference_sequence&amp;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 &amp;lt;input_file&amp;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 &amp;lt;reference_sequence&amp;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 &amp;lt;calculateCoverageOverGenes&amp;gt;" />
154
155 <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;">
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 &amp;lt;summaryCoverageThreshold&amp;gt;">
162 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
163 </repeat>
164
165 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;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 &amp;lt;maxBaseQuality&amp;gt;" />
177 <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;" />
178 <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;" />
179 <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;" />
180 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &amp;lt;nBins&amp;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 &amp;lt;start&amp;gt;" />
188 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;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 &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html&gt;`_.
696
697 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;`_.
698
699 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
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 &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ 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>