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comparison depth_of_coverage.xml @ 0:6d46b7a39a08 draft default tip

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Imported from capsule None
author devteam
date Tue, 01 Apr 2014 09:12:33 -0400
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-1:000000000000 0:6d46b7a39a08
1 <tool id="gatk_depth_of_coverage" name="Depth of Coverage" version="0.0.2">
2 <description>on BAM files</description>
3 <requirements>
4 <requirement type="package" version="1.4">gatk</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement>
6 </requirements>
7 <macros>
8 <import>gatk_macros.xml</import>
9 </macros>
10 <command interpreter="python">gatk_wrapper.py
11 --max_jvm_heap_fraction "1"
12 --stdout "${output_log}"
13 #for $i, $input_bam in enumerate( $reference_source.input_bams ):
14 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
15 #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
16 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
17 #end if
18 #end for
19 -p 'java
20 -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
21 -T "DepthOfCoverage"
22 ##--num_threads 4 ##hard coded, for now
23
24 -et "NO_ET" ##ET no phone home
25 #if $reference_source.reference_source_selector != "history":
26 -R "${reference_source.ref_file.fields.path}"
27 #end if
28 #if str( $input_calculate_coverage_over_genes ) != "None":
29 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}"
30 #end if
31 #if str( $partition_type ) != "None":
32 #for $pt in str( $partition_type ).split( ',' ):
33 --partitionType "${pt}"
34 #end for
35 #end if
36 --out "${output_per_locus_coverage}"
37
38 #for $ct_group in $summary_coverage_threshold_group:
39 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
40 #end for
41 --outputFormat "${output_format}"
42 '
43
44 #include source=$standard_gatk_options#
45 ##start analysis specific options
46 #if $analysis_param_type.analysis_param_type_selector == "advanced":
47 -p '
48 ${analysis_param_type.ignore_deletion_sites}
49 ${analysis_param_type.include_deletions}
50 --maxBaseQuality "${analysis_param_type.max_base_quality}"
51 --maxMappingQuality "${analysis_param_type.max_mapping_quality}"
52 --minBaseQuality "${analysis_param_type.min_base_quality}"
53 --minMappingQuality "${analysis_param_type.min_mapping_quality}"
54 --nBins "${analysis_param_type.n_bins}"
55 ${analysis_param_type.omit_depth_output_at_each_base}
56 ${analysis_param_type.omit_interval_statistics}
57 ${analysis_param_type.omit_locus_table}
58 ${analysis_param_type.omit_per_sample_stats}
59 ${analysis_param_type.print_base_counts}
60 ${analysis_param_type.print_bin_endpoints_and_exit}
61 --start "${analysis_param_type.start}"
62 --stop "${analysis_param_type.stop}"
63 '
64 #end if
65 ##Move additional files to final location
66 #if str( $partition_type ) != "None":
67 #set $partition_types = str( $partition_type ).split( ',' )
68 #else:
69 #set $partition_types = [ 'sample' ]
70 #end if
71 #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 ) == "" ):
72 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
73 &amp;&amp; mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
74 &amp;&amp; mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample}
75 #end if
76 #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 ) == "" ):
77 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
78 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
79 #end if
80 #if str( $input_calculate_coverage_over_genes ) != "None":
81 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
82 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample}
83 #end if
84 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
85 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
86 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
87 #end if
88 #end if
89
90 #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 ) == "" ):
91 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
92 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
93 &amp;&amp; mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
94 #end if
95 #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 ) == "" ):
96 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
97 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
98 #end if
99 #if str( $input_calculate_coverage_over_genes ) != "None":
100 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
101 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup}
102 #end if
103 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
104 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
105 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
106 #end if
107 #end if
108
109 #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 ) == "" ):
110 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
111 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
112 &amp;&amp; mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
113 #end if
114 #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 ) == "" ):
115 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
116 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
117 #end if
118 #if str( $input_calculate_coverage_over_genes ) != "None":
119 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
120 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library}
121 #end if
122 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
123 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
124 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
125 #end if
126 #end if
127
128
129 </command>
130 <inputs>
131 <conditional name="reference_source">
132 <expand macro="reference_source_selector_param" />
133 <when value="cached">
134 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
135 <param name="input_bam" type="data" format="bam" label="BAM file">
136 <validator type="unspecified_build" />
137 <validator type="dataset_metadata_in_data_table" table_name="gatk_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 -->
138 </param>
139 </repeat>
140 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
141 <options from_data_table="gatk_picard_indexes">
142 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
143 </options>
144 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
145 </param>
146 </when>
147 <when value="history"> <!-- FIX ME!!!! -->
148 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
149 <param name="input_bam" type="data" format="bam" label="BAM file" />
150 </repeat>
151 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
152 </when>
153 </conditional>
154
155 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />
156
157 <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;">
158 <option value="sample" selected="True">sample</option>
159 <option value="readgroup">readgroup</option>
160 <option value="library">library</option>
161 </param>
162
163 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;">
164 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
165 </repeat>
166
167 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" >
168 <option value="csv">csv</option>
169 <option value="table">table</option>
170 <option value="rtable" selected="True">rtable</option>
171 </param>
172
173 <expand macro="gatk_param_type_conditional" />
174
175 <expand macro="analysis_type_conditional">
176 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
177 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
178 <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;" />
179 <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;" />
180 <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;" />
181 <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;" />
182 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &amp;lt;nBins&amp;gt;" />
183 <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" />
184 <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" />
185 <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" />
186 <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" />
187 <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" />
188 <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
189 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &amp;lt;start&amp;gt;" />
190 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;gt;" />
191 </expand>
192 </inputs>
193 <outputs>
194 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
195 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
196 <actions>
197 <conditional name="output_format">
198 <when value="rtable">
199 <action type="format">
200 <option type="from_param" name="output_format" />
201 </action>
202 </when>
203 <when value="csv">
204 <action type="format">
205 <option type="from_param" name="output_format" />
206 </action>
207 </when>
208 </conditional>
209 </actions>
210 </data>
211 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" >
212 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
213 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
214 <filter>'sample' in partition_type or not partition_type</filter>
215 <actions>
216 <conditional name="output_format">
217 <when value="rtable">
218 <action type="format">
219 <option type="from_param" name="output_format" />
220 </action>
221 </when>
222 <when value="csv">
223 <action type="format">
224 <option type="from_param" name="output_format" />
225 </action>
226 </when>
227 </conditional>
228 </actions>
229 </data>
230 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" >
231 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
232 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
233 <filter>'sample' in partition_type or not partition_type</filter>
234 <actions>
235 <conditional name="output_format">
236 <when value="rtable">
237 <action type="format">
238 <option type="from_param" name="output_format" />
239 </action>
240 </when>
241 <when value="csv">
242 <action type="format">
243 <option type="from_param" name="output_format" />
244 </action>
245 </when>
246 </conditional>
247 </actions>
248 </data>
249 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" >
250 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
251 <filter>'sample' in partition_type or not partition_type</filter>
252 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
253 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
254 <actions>
255 <conditional name="output_format">
256 <when value="rtable">
257 <action type="format">
258 <option type="from_param" name="output_format" />
259 </action>
260 </when>
261 <when value="csv">
262 <action type="format">
263 <option type="from_param" name="output_format" />
264 </action>
265 </when>
266 </conditional>
267 </actions>
268 </data>
269 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" >
270 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
271 <filter>'sample' in partition_type or not partition_type</filter>
272 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
273 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
274 <actions>
275 <conditional name="output_format">
276 <when value="rtable">
277 <action type="format">
278 <option type="from_param" name="output_format" />
279 </action>
280 </when>
281 <when value="csv">
282 <action type="format">
283 <option type="from_param" name="output_format" />
284 </action>
285 </when>
286 </conditional>
287 </actions>
288 </data>
289 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" >
290 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
291 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
292 <actions>
293 <conditional name="output_format">
294 <when value="rtable">
295 <action type="format">
296 <option type="from_param" name="output_format" />
297 </action>
298 </when>
299 <when value="csv">
300 <action type="format">
301 <option type="from_param" name="output_format" />
302 </action>
303 </when>
304 </conditional>
305 </actions>
306 </data>
307 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" >
308 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
309 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
310 <actions>
311 <conditional name="output_format">
312 <when value="rtable">
313 <action type="format">
314 <option type="from_param" name="output_format" />
315 </action>
316 </when>
317 <when value="csv">
318 <action type="format">
319 <option type="from_param" name="output_format" />
320 </action>
321 </when>
322 </conditional>
323 </actions>
324 </data>
325 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" >
326 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
327 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
328 <filter>'sample' in partition_type or not partition_type</filter>
329 <actions>
330 <conditional name="output_format">
331 <when value="rtable">
332 <action type="format">
333 <option type="from_param" name="output_format" />
334 </action>
335 </when>
336 <when value="csv">
337 <action type="format">
338 <option type="from_param" name="output_format" />
339 </action>
340 </when>
341 </conditional>
342 </actions>
343 </data>
344 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" >
345 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
346 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
347 <filter>'sample' in partition_type or not partition_type</filter>
348 <actions>
349 <conditional name="output_format">
350 <when value="rtable">
351 <action type="format">
352 <option type="from_param" name="output_format" />
353 </action>
354 </when>
355 <when value="csv">
356 <action type="format">
357 <option type="from_param" name="output_format" />
358 </action>
359 </when>
360 </conditional>
361 </actions>
362 </data>
363
364 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
365 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
366 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
367 <filter>'readgroup' in partition_type</filter>
368 <actions>
369 <conditional name="output_format">
370 <when value="rtable">
371 <action type="format">
372 <option type="from_param" name="output_format" />
373 </action>
374 </when>
375 <when value="csv">
376 <action type="format">
377 <option type="from_param" name="output_format" />
378 </action>
379 </when>
380 </conditional>
381 </actions>
382 </data>
383 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" >
384 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
385 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
386 <filter>'readgroup' in partition_type</filter>
387 <actions>
388 <conditional name="output_format">
389 <when value="rtable">
390 <action type="format">
391 <option type="from_param" name="output_format" />
392 </action>
393 </when>
394 <when value="csv">
395 <action type="format">
396 <option type="from_param" name="output_format" />
397 </action>
398 </when>
399 </conditional>
400 </actions>
401 </data>
402 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" >
403 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
404 <filter>'readgroup' in partition_type</filter>
405 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
406 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
407 <actions>
408 <conditional name="output_format">
409 <when value="rtable">
410 <action type="format">
411 <option type="from_param" name="output_format" />
412 </action>
413 </when>
414 <when value="csv">
415 <action type="format">
416 <option type="from_param" name="output_format" />
417 </action>
418 </when>
419 </conditional>
420 </actions>
421 </data>
422 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" >
423 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
424 <filter>'readgroup' in partition_type</filter>
425 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
426 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
427 <actions>
428 <conditional name="output_format">
429 <when value="rtable">
430 <action type="format">
431 <option type="from_param" name="output_format" />
432 </action>
433 </when>
434 <when value="csv">
435 <action type="format">
436 <option type="from_param" name="output_format" />
437 </action>
438 </when>
439 </conditional>
440 </actions>
441 </data>
442 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" >
443 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
444 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
445 <actions>
446 <conditional name="output_format">
447 <when value="rtable">
448 <action type="format">
449 <option type="from_param" name="output_format" />
450 </action>
451 </when>
452 <when value="csv">
453 <action type="format">
454 <option type="from_param" name="output_format" />
455 </action>
456 </when>
457 </conditional>
458 </actions>
459 </data>
460 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" >
461 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
462 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
463 <actions>
464 <conditional name="output_format">
465 <when value="rtable">
466 <action type="format">
467 <option type="from_param" name="output_format" />
468 </action>
469 </when>
470 <when value="csv">
471 <action type="format">
472 <option type="from_param" name="output_format" />
473 </action>
474 </when>
475 </conditional>
476 </actions>
477 </data>
478 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" >
479 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
480 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
481 <filter>'readgroup' in partition_type</filter>
482 <actions>
483 <conditional name="output_format">
484 <when value="rtable">
485 <action type="format">
486 <option type="from_param" name="output_format" />
487 </action>
488 </when>
489 <when value="csv">
490 <action type="format">
491 <option type="from_param" name="output_format" />
492 </action>
493 </when>
494 </conditional>
495 </actions>
496 </data>
497 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" >
498 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
499 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
500 <filter>'readgroup' in partition_type</filter>
501 <actions>
502 <conditional name="output_format">
503 <when value="rtable">
504 <action type="format">
505 <option type="from_param" name="output_format" />
506 </action>
507 </when>
508 <when value="csv">
509 <action type="format">
510 <option type="from_param" name="output_format" />
511 </action>
512 </when>
513 </conditional>
514 </actions>
515 </data>
516
517 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
518 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
519 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
520 <filter>'library' in partition_type</filter>
521 <actions>
522 <conditional name="output_format">
523 <when value="rtable">
524 <action type="format">
525 <option type="from_param" name="output_format" />
526 </action>
527 </when>
528 <when value="csv">
529 <action type="format">
530 <option type="from_param" name="output_format" />
531 </action>
532 </when>
533 </conditional>
534 </actions>
535 </data>
536 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" >
537 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
538 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
539 <filter>'library' in partition_type</filter>
540 <actions>
541 <conditional name="output_format">
542 <when value="rtable">
543 <action type="format">
544 <option type="from_param" name="output_format" />
545 </action>
546 </when>
547 <when value="csv">
548 <action type="format">
549 <option type="from_param" name="output_format" />
550 </action>
551 </when>
552 </conditional>
553 </actions>
554 </data>
555 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" >
556 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
557 <filter>'library' in partition_type</filter>
558 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
559 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
560 <actions>
561 <conditional name="output_format">
562 <when value="rtable">
563 <action type="format">
564 <option type="from_param" name="output_format" />
565 </action>
566 </when>
567 <when value="csv">
568 <action type="format">
569 <option type="from_param" name="output_format" />
570 </action>
571 </when>
572 </conditional>
573 </actions>
574 </data>
575 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" >
576 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
577 <filter>'library' in partition_type</filter>
578 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
579 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
580 <actions>
581 <conditional name="output_format">
582 <when value="rtable">
583 <action type="format">
584 <option type="from_param" name="output_format" />
585 </action>
586 </when>
587 <when value="csv">
588 <action type="format">
589 <option type="from_param" name="output_format" />
590 </action>
591 </when>
592 </conditional>
593 </actions>
594 </data>
595 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" >
596 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
597 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
598 <actions>
599 <conditional name="output_format">
600 <when value="rtable">
601 <action type="format">
602 <option type="from_param" name="output_format" />
603 </action>
604 </when>
605 <when value="csv">
606 <action type="format">
607 <option type="from_param" name="output_format" />
608 </action>
609 </when>
610 </conditional>
611 </actions>
612 </data>
613 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" >
614 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
615 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
616 <actions>
617 <conditional name="output_format">
618 <when value="rtable">
619 <action type="format">
620 <option type="from_param" name="output_format" />
621 </action>
622 </when>
623 <when value="csv">
624 <action type="format">
625 <option type="from_param" name="output_format" />
626 </action>
627 </when>
628 </conditional>
629 </actions>
630 </data>
631 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" >
632 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
633 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
634 <filter>'library' in partition_type</filter>
635 <actions>
636 <conditional name="output_format">
637 <when value="rtable">
638 <action type="format">
639 <option type="from_param" name="output_format" />
640 </action>
641 </when>
642 <when value="csv">
643 <action type="format">
644 <option type="from_param" name="output_format" />
645 </action>
646 </when>
647 </conditional>
648 </actions>
649 </data>
650 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" >
651 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
652 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
653 <filter>'library' in partition_type</filter>
654 <actions>
655 <conditional name="output_format">
656 <when value="rtable">
657 <action type="format">
658 <option type="from_param" name="output_format" />
659 </action>
660 </when>
661 <when value="csv">
662 <action type="format">
663 <option type="from_param" name="output_format" />
664 </action>
665 </when>
666 </conditional>
667 </actions>
668 </data>
669
670 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
671 </outputs>
672 <trackster_conf/>
673 <tests>
674 <test>
675 <param name="reference_source_selector" value="history" />
676 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
677 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
678 <param name="input_calculate_coverage_over_genes" />
679 <param name="partition_type" value="sample" />
680 <param name="summary_coverage_threshold_group" value="0" />
681 <param name="output_format" value="rtable" />
682 <param name="gatk_param_type_selector" value="basic" />
683 <param name="analysis_param_type_selector" value="basic" />
684 <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" />
685 <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" />
686 <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" />
687 <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" />
688 <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" />
689 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" />
690 </test>
691 </tests>
692 <help>
693 **What it does**
694
695 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.
696
697 For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Depth_of_Coverage&gt;`_.
698
699 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3&gt;`_.
700
701 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
702
703 ------
704
705 **Inputs**
706
707 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.
708
709
710 **Outputs**
711
712 The output is in various table formats.
713
714
715 Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
716
717 -------
718
719 **Settings**::
720
721 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
722 ignoreDeletionSites boolean false Ignore sites consisting only of deletions
723 includeDeletions boolean false Include information on deletions
724 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
725 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
726 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
727 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
728 nBins int 499 Number of bins to use for granular binning
729 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
730 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
731 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
732 omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
733 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
734 partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
735 printBaseCounts boolean false Will add base counts to per-locus output.
736 printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
737 start int 1 Starting (left endpoint) for granular binning
738 stop int 500 Ending (right endpoint) for granular binning
739 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
740
741 @CITATION_SECTION@
742 </help>
743 </tool>