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comparison depth_of_coverage.xml @ 11:432aafa6830a draft

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author david-hoover
date Wed, 12 Sep 2012 17:54:46 -0400
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10:b138c5569231 11:432aafa6830a
1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.1">
2 <description>on BAM files</description>
3 <requirements>
4 <requirement type="package" version="2.1">gatk</requirement>
5 <requirement type="package">samtools</requirement>
6 </requirements>
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 'java
17 -jar "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/GenomeAnalysisTK.jar"
18 -T "DepthOfCoverage"
19 ##--num_threads 4 ##hard coded, for now
20
21 -et "NO_ET" -K "/data/galaxy/galaxy3/tool-data/shared/jars/gatk2/gatk2_key_file" ##ET no phone home
22 #if $reference_source.reference_source_selector != "history":
23 -R "${reference_source.ref_file.fields.path}"
24 #end if
25 #if str( $input_calculate_coverage_over_genes ) != "None":
26 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}"
27 #end if
28 #if str( $partition_type ) != "None":
29 #for $pt in str( $partition_type ).split( ',' ):
30 --partitionType "${pt}"
31 #end for
32 #end if
33 --out "${output_per_locus_coverage}"
34
35 #for $ct_group in $summary_coverage_threshold_group:
36 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
37 #end for
38 --outputFormat "${output_format}"
39 '
40
41 ##start standard gatk options
42 #if $gatk_param_type.gatk_param_type_selector == "advanced":
43 #for $pedigree in $gatk_param_type.pedigree:
44 -p '--pedigree "${pedigree.pedigree_file}"'
45 #end for
46 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
47 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
48 #end for
49 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
50 #for $read_filter in $gatk_param_type.read_filter:
51 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
52 ###raise Exception( str( dir( $read_filter ) ) )
53 #for $name, $param in $read_filter.read_filter_type.iteritems():
54 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
55 #if hasattr( $param.input, 'truevalue' ):
56 ${param}
57 #else:
58 --${name} "${param}"
59 #end if
60 #end if
61 #end for
62 '
63 #end for
64 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
65 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
66 #end for
67
68 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
69 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
70 #end for
71
72 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
73
74 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
75 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
76 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
77 #end if
78 -p '
79 --baq "${gatk_param_type.baq}"
80 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
81 ${gatk_param_type.use_original_qualities}
82 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
83 --validation_strictness "${gatk_param_type.validation_strictness}"
84 --interval_merging "${gatk_param_type.interval_merging}"
85 ${gatk_param_type.disable_experimental_low_memory_sharding}
86 ${gatk_param_type.non_deterministic_random_seed}
87 '
88 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
89 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
90 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
91 #else
92 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
93 #end if
94 #end for
95 #end if
96
97 #if $reference_source.reference_source_selector == "history":
98 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
99 #end if
100 ##end standard gatk options
101 ##start analysis specific options
102 #if $analysis_param_type.analysis_param_type_selector == "advanced":
103 -p '
104 ${analysis_param_type.ignore_deletion_sites}
105 ${analysis_param_type.include_deletions}
106 --maxBaseQuality "${analysis_param_type.max_base_quality}"
107 --maxMappingQuality "${analysis_param_type.max_mapping_quality}"
108 --minBaseQuality "${analysis_param_type.min_base_quality}"
109 --minMappingQuality "${analysis_param_type.min_mapping_quality}"
110 --nBins "${analysis_param_type.n_bins}"
111 ${analysis_param_type.omit_depth_output_at_each_base}
112 ${analysis_param_type.omit_interval_statistics}
113 ${analysis_param_type.omit_locus_table}
114 ${analysis_param_type.omit_per_sample_stats}
115 ${analysis_param_type.print_base_counts}
116 ${analysis_param_type.print_bin_endpoints_and_exit}
117 --start "${analysis_param_type.start}"
118 --stop "${analysis_param_type.stop}"
119 '
120 #end if
121 ##Move additional files to final location
122 #if str( $partition_type ) != "None":
123 #set $partition_types = str( $partition_type ).split( ',' )
124 #else:
125 #set $partition_types = [ 'sample' ]
126 #end if
127 #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 ) == "" ):
128 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
129 &amp;&amp; mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
130 &amp;&amp; mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample}
131 #end if
132 #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 ) == "" ):
133 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
134 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
135 #end if
136 #if str( $input_calculate_coverage_over_genes ) != "None":
137 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
138 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample}
139 #end if
140 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
141 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
142 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
143 #end if
144 #end if
145
146 #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 ) == "" ):
147 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
148 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
149 &amp;&amp; mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
150 #end if
151 #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 ) == "" ):
152 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
153 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
154 #end if
155 #if str( $input_calculate_coverage_over_genes ) != "None":
156 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
157 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup}
158 #end if
159 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
160 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
161 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
162 #end if
163 #end if
164
165 #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 ) == "" ):
166 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
167 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
168 &amp;&amp; mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
169 #end if
170 #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 ) == "" ):
171 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
172 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
173 #end if
174 #if str( $input_calculate_coverage_over_genes ) != "None":
175 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
176 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library}
177 #end if
178 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
179 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
180 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
181 #end if
182 #end if
183
184
185 </command>
186 <inputs>
187 <conditional name="reference_source">
188 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
189 <option value="cached">Locally cached</option>
190 <option value="history">History</option>
191 </param>
192 <when value="cached">
193 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
194 <param name="input_bam" type="data" format="bam" label="BAM file">
195 <validator type="unspecified_build" />
196 <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 -->
197 </param>
198 </repeat>
199 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
200 <options from_data_table="gatk2_picard_indexes">
201 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
202 </options>
203 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
204 </param>
205 </when>
206 <when value="history"> <!-- FIX ME!!!! -->
207 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
208 <param name="input_bam" type="data" format="bam" label="BAM file" />
209 </repeat>
210 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
211 </when>
212 </conditional>
213
214 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />
215
216 <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;">
217 <option value="sample" selected="True">sample</option>
218 <option value="readgroup">readgroup</option>
219 <option value="library">library</option>
220 </param>
221
222 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;">
223 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
224 </repeat>
225
226 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" >
227 <option value="csv">csv</option>
228 <option value="table">table</option>
229 <option value="rtable" selected="True">rtable</option>
230 </param>
231
232 <conditional name="gatk_param_type">
233 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
234 <option value="basic" selected="True">Basic</option>
235 <option value="advanced">Advanced</option>
236 </param>
237 <when value="basic">
238 <!-- Do nothing here -->
239 </when>
240 <when value="advanced">
241 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
242 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
243 </repeat>
244 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
245 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
246 </repeat>
247 <param name="pedigree_validation_type" type="select" label="How strict should we be in validating the pedigree information" help="-pedValidationType,--pedigreeValidationType &amp;lt;pedigreeValidationType&amp;gt;">
248 <option value="STRICT" selected="True">STRICT</option>
249 <option value="SILENT">SILENT</option>
250 </param>
251 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
252 <conditional name="read_filter_type">
253 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
254 <option value="BadCigar">BadCigar</option>
255 <option value="BadMate">BadMate</option>
256 <option value="DuplicateRead">DuplicateRead</option>
257 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
258 <option value="MalformedRead">MalformedRead</option>
259 <option value="MappingQuality">MappingQuality</option>
260 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
261 <option value="MappingQualityZero">MappingQualityZero</option>
262 <option value="MateSameStrand">MateSameStrand</option>
263 <option value="MaxInsertSize">MaxInsertSize</option>
264 <option value="MaxReadLength" selected="True">MaxReadLength</option>
265 <option value="MissingReadGroup">MissingReadGroup</option>
266 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
267 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
268 <option value="Platform454">Platform454</option>
269 <option value="Platform">Platform</option>
270 <option value="PlatformUnit">PlatformUnit</option>
271 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
272 <option value="ReadName">ReadName</option>
273 <option value="ReadStrand">ReadStrand</option>
274 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
275 <option value="Sample">Sample</option>
276 <option value="SingleReadGroup">SingleReadGroup</option>
277 <option value="UnmappedRead">UnmappedRead</option>
278 </param>
279 <when value="BadCigar">
280 <!-- no extra options -->
281 </when>
282 <when value="BadMate">
283 <!-- no extra options -->
284 </when>
285 <when value="DuplicateRead">
286 <!-- no extra options -->
287 </when>
288 <when value="FailsVendorQualityCheck">
289 <!-- no extra options -->
290 </when>
291 <when value="MalformedRead">
292 <!-- no extra options -->
293 </when>
294 <when value="MappingQuality">
295 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
296 </when>
297 <when value="MappingQualityUnavailable">
298 <!-- no extra options -->
299 </when>
300 <when value="MappingQualityZero">
301 <!-- no extra options -->
302 </when>
303 <when value="MateSameStrand">
304 <!-- no extra options -->
305 </when>
306 <when value="MaxInsertSize">
307 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
308 </when>
309 <when value="MaxReadLength">
310 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
311 </when>
312 <when value="MissingReadGroup">
313 <!-- no extra options -->
314 </when>
315 <when value="NoOriginalQualityScores">
316 <!-- no extra options -->
317 </when>
318 <when value="NotPrimaryAlignment">
319 <!-- no extra options -->
320 </when>
321 <when value="Platform454">
322 <!-- no extra options -->
323 </when>
324 <when value="Platform">
325 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
326 </when>
327 <when value="PlatformUnit">
328 <!-- no extra options -->
329 </when>
330 <when value="ReadGroupBlackList">
331 <!-- no extra options -->
332 </when>
333 <when value="ReadName">
334 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
335 </when>
336 <when value="ReadStrand">
337 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
338 </when>
339 <when value="ReassignMappingQuality">
340 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
341 </when>
342 <when value="Sample">
343 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
344 </when>
345 <when value="SingleReadGroup">
346 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
347 </when>
348 <when value="UnmappedRead">
349 <!-- no extra options -->
350 </when>
351 </conditional>
352 </repeat>
353 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
354 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
355 </repeat>
356 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
357 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
358 </repeat>
359
360 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
361 <option value="UNION" selected="True">UNION</option>
362 <option value="INTERSECTION">INTERSECTION</option>
363 </param>
364
365 <conditional name="downsampling_type">
366 <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="-dt,--downsampling_type &amp;lt;downsampling_type&amp;gt;">
367 <option value="NONE" selected="True">NONE</option>
368 <option value="ALL_READS">ALL_READS</option>
369 <option value="BY_SAMPLE">BY_SAMPLE</option>
370 </param>
371 <when value="NONE">
372 <!-- no more options here -->
373 </when>
374 <when value="ALL_READS">
375 <conditional name="downsample_to_type">
376 <param name="downsample_to_type_selector" type="select" label="Downsample method">
377 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
378 <option value="downsample_to_coverage">Downsample by Coverage</option>
379 </param>
380 <when value="downsample_to_fraction">
381 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
382 </when>
383 <when value="downsample_to_coverage">
384 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
385 </when>
386 </conditional>
387 </when>
388 <when value="BY_SAMPLE">
389 <conditional name="downsample_to_type">
390 <param name="downsample_to_type_selector" type="select" label="Downsample method">
391 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
392 <option value="downsample_to_coverage">Downsample by Coverage</option>
393 </param>
394 <when value="downsample_to_fraction">
395 <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="1" min="0" max="1" help="-dfrac,--downsample_to_fraction &amp;lt;downsample_to_fraction&amp;gt;"/>
396 </when>
397 <when value="downsample_to_coverage">
398 <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0" help="-dcov,--downsample_to_coverage &amp;lt;downsample_to_coverage&amp;gt;"/>
399 </when>
400 </conditional>
401 </when>
402 </conditional>
403 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
404 <option value="OFF" selected="True">OFF</option>
405 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
406 <option value="RECALCULATE">RECALCULATE</option>
407 </param>
408 <param name="baq_gap_open_penalty" type="float" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets. -baqGOP,--baqGapOpenPenalty &amp;lt;baqGapOpenPenalty&amp;gt;" />
409 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
410 <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1" help="-DBQ,--defaultBaseQualities &amp;lt;defaultBaseQualities&amp;gt;"/>
411 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
412 <option value="STRICT" selected="True">STRICT</option>
413 <option value="LENIENT">LENIENT</option>
414 <option value="SILENT">SILENT</option>
415 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
416 </param>
417 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
418 <option value="ALL" selected="True">ALL</option>
419 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
420 </param>
421
422 <repeat name="read_group_black_list_repeat" title="Read group black list" help="-rgbl,--read_group_black_list &amp;lt;read_group_black_list&amp;gt;">
423 <conditional name="read_group_black_list_type">
424 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
425 <option value="file" selected="True">Filters in file</option>
426 <option value="text">Specify filters as a string</option>
427 </param>
428 <when value="file">
429 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
430 </when>
431 <when value="text">
432 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
433 </when>
434 </conditional>
435 </repeat>
436
437 <param name="disable_experimental_low_memory_sharding" type="boolean" truevalue="--disable_experimental_low_memory_sharding" falsevalue="" label="Disable experimental low-memory sharding functionality." checked="False" help="--disable_experimental_low_memory_sharding"/>
438 <param name="non_deterministic_random_seed" type="boolean" truevalue="--nonDeterministicRandomSeed" falsevalue="" label="Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run" checked="False" help="-ndrs,--nonDeterministicRandomSeed"/>
439
440 </when>
441 </conditional>
442
443 <conditional name="analysis_param_type">
444 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
445 <option value="basic" selected="True">Basic</option>
446 <option value="advanced">Advanced</option>
447 </param>
448 <when value="basic">
449 <!-- Do nothing here -->
450 </when>
451 <when value="advanced">
452 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
453 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
454 <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;" />
455 <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;" />
456 <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;" />
457 <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;" />
458 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &amp;lt;nBins&amp;gt;" />
459 <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" />
460 <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" />
461 <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" />
462 <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" />
463 <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" />
464 <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
465 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &amp;lt;start&amp;gt;" />
466 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;gt;" />
467 </when>
468 </conditional>
469 </inputs>
470 <outputs>
471 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
472 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
473 <actions>
474 <conditional name="output_format">
475 <when value="rtable">
476 <action type="format">
477 <option type="from_param" name="output_format" />
478 </action>
479 </when>
480 <when value="csv">
481 <action type="format">
482 <option type="from_param" name="output_format" />
483 </action>
484 </when>
485 </conditional>
486 </actions>
487 </data>
488 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" >
489 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
490 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
491 <filter>'sample' in partition_type or not partition_type</filter>
492 <actions>
493 <conditional name="output_format">
494 <when value="rtable">
495 <action type="format">
496 <option type="from_param" name="output_format" />
497 </action>
498 </when>
499 <when value="csv">
500 <action type="format">
501 <option type="from_param" name="output_format" />
502 </action>
503 </when>
504 </conditional>
505 </actions>
506 </data>
507 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" >
508 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
509 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
510 <filter>'sample' in partition_type or not partition_type</filter>
511 <actions>
512 <conditional name="output_format">
513 <when value="rtable">
514 <action type="format">
515 <option type="from_param" name="output_format" />
516 </action>
517 </when>
518 <when value="csv">
519 <action type="format">
520 <option type="from_param" name="output_format" />
521 </action>
522 </when>
523 </conditional>
524 </actions>
525 </data>
526 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" >
527 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
528 <filter>'sample' in partition_type or not partition_type</filter>
529 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
530 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
531 <actions>
532 <conditional name="output_format">
533 <when value="rtable">
534 <action type="format">
535 <option type="from_param" name="output_format" />
536 </action>
537 </when>
538 <when value="csv">
539 <action type="format">
540 <option type="from_param" name="output_format" />
541 </action>
542 </when>
543 </conditional>
544 </actions>
545 </data>
546 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" >
547 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
548 <filter>'sample' in partition_type or not partition_type</filter>
549 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
550 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
551 <actions>
552 <conditional name="output_format">
553 <when value="rtable">
554 <action type="format">
555 <option type="from_param" name="output_format" />
556 </action>
557 </when>
558 <when value="csv">
559 <action type="format">
560 <option type="from_param" name="output_format" />
561 </action>
562 </when>
563 </conditional>
564 </actions>
565 </data>
566 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" >
567 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
568 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
569 <actions>
570 <conditional name="output_format">
571 <when value="rtable">
572 <action type="format">
573 <option type="from_param" name="output_format" />
574 </action>
575 </when>
576 <when value="csv">
577 <action type="format">
578 <option type="from_param" name="output_format" />
579 </action>
580 </when>
581 </conditional>
582 </actions>
583 </data>
584 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" >
585 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
586 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
587 <actions>
588 <conditional name="output_format">
589 <when value="rtable">
590 <action type="format">
591 <option type="from_param" name="output_format" />
592 </action>
593 </when>
594 <when value="csv">
595 <action type="format">
596 <option type="from_param" name="output_format" />
597 </action>
598 </when>
599 </conditional>
600 </actions>
601 </data>
602 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" >
603 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
604 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
605 <filter>'sample' in partition_type or not partition_type</filter>
606 <actions>
607 <conditional name="output_format">
608 <when value="rtable">
609 <action type="format">
610 <option type="from_param" name="output_format" />
611 </action>
612 </when>
613 <when value="csv">
614 <action type="format">
615 <option type="from_param" name="output_format" />
616 </action>
617 </when>
618 </conditional>
619 </actions>
620 </data>
621 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" >
622 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
623 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
624 <filter>'sample' in partition_type or not partition_type</filter>
625 <actions>
626 <conditional name="output_format">
627 <when value="rtable">
628 <action type="format">
629 <option type="from_param" name="output_format" />
630 </action>
631 </when>
632 <when value="csv">
633 <action type="format">
634 <option type="from_param" name="output_format" />
635 </action>
636 </when>
637 </conditional>
638 </actions>
639 </data>
640
641 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
642 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
643 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
644 <filter>'readgroup' in partition_type</filter>
645 <actions>
646 <conditional name="output_format">
647 <when value="rtable">
648 <action type="format">
649 <option type="from_param" name="output_format" />
650 </action>
651 </when>
652 <when value="csv">
653 <action type="format">
654 <option type="from_param" name="output_format" />
655 </action>
656 </when>
657 </conditional>
658 </actions>
659 </data>
660 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" >
661 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
662 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
663 <filter>'readgroup' in partition_type</filter>
664 <actions>
665 <conditional name="output_format">
666 <when value="rtable">
667 <action type="format">
668 <option type="from_param" name="output_format" />
669 </action>
670 </when>
671 <when value="csv">
672 <action type="format">
673 <option type="from_param" name="output_format" />
674 </action>
675 </when>
676 </conditional>
677 </actions>
678 </data>
679 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" >
680 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
681 <filter>'readgroup' in partition_type</filter>
682 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
683 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
684 <actions>
685 <conditional name="output_format">
686 <when value="rtable">
687 <action type="format">
688 <option type="from_param" name="output_format" />
689 </action>
690 </when>
691 <when value="csv">
692 <action type="format">
693 <option type="from_param" name="output_format" />
694 </action>
695 </when>
696 </conditional>
697 </actions>
698 </data>
699 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" >
700 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
701 <filter>'readgroup' in partition_type</filter>
702 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
703 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
704 <actions>
705 <conditional name="output_format">
706 <when value="rtable">
707 <action type="format">
708 <option type="from_param" name="output_format" />
709 </action>
710 </when>
711 <when value="csv">
712 <action type="format">
713 <option type="from_param" name="output_format" />
714 </action>
715 </when>
716 </conditional>
717 </actions>
718 </data>
719 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" >
720 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
721 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
722 <actions>
723 <conditional name="output_format">
724 <when value="rtable">
725 <action type="format">
726 <option type="from_param" name="output_format" />
727 </action>
728 </when>
729 <when value="csv">
730 <action type="format">
731 <option type="from_param" name="output_format" />
732 </action>
733 </when>
734 </conditional>
735 </actions>
736 </data>
737 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" >
738 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
739 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
740 <actions>
741 <conditional name="output_format">
742 <when value="rtable">
743 <action type="format">
744 <option type="from_param" name="output_format" />
745 </action>
746 </when>
747 <when value="csv">
748 <action type="format">
749 <option type="from_param" name="output_format" />
750 </action>
751 </when>
752 </conditional>
753 </actions>
754 </data>
755 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" >
756 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
757 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
758 <filter>'readgroup' in partition_type</filter>
759 <actions>
760 <conditional name="output_format">
761 <when value="rtable">
762 <action type="format">
763 <option type="from_param" name="output_format" />
764 </action>
765 </when>
766 <when value="csv">
767 <action type="format">
768 <option type="from_param" name="output_format" />
769 </action>
770 </when>
771 </conditional>
772 </actions>
773 </data>
774 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" >
775 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
776 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
777 <filter>'readgroup' in partition_type</filter>
778 <actions>
779 <conditional name="output_format">
780 <when value="rtable">
781 <action type="format">
782 <option type="from_param" name="output_format" />
783 </action>
784 </when>
785 <when value="csv">
786 <action type="format">
787 <option type="from_param" name="output_format" />
788 </action>
789 </when>
790 </conditional>
791 </actions>
792 </data>
793
794 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
795 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
796 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
797 <filter>'library' in partition_type</filter>
798 <actions>
799 <conditional name="output_format">
800 <when value="rtable">
801 <action type="format">
802 <option type="from_param" name="output_format" />
803 </action>
804 </when>
805 <when value="csv">
806 <action type="format">
807 <option type="from_param" name="output_format" />
808 </action>
809 </when>
810 </conditional>
811 </actions>
812 </data>
813 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" >
814 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
815 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
816 <filter>'library' in partition_type</filter>
817 <actions>
818 <conditional name="output_format">
819 <when value="rtable">
820 <action type="format">
821 <option type="from_param" name="output_format" />
822 </action>
823 </when>
824 <when value="csv">
825 <action type="format">
826 <option type="from_param" name="output_format" />
827 </action>
828 </when>
829 </conditional>
830 </actions>
831 </data>
832 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" >
833 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
834 <filter>'library' in partition_type</filter>
835 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
836 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
837 <actions>
838 <conditional name="output_format">
839 <when value="rtable">
840 <action type="format">
841 <option type="from_param" name="output_format" />
842 </action>
843 </when>
844 <when value="csv">
845 <action type="format">
846 <option type="from_param" name="output_format" />
847 </action>
848 </when>
849 </conditional>
850 </actions>
851 </data>
852 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" >
853 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
854 <filter>'library' in partition_type</filter>
855 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
856 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
857 <actions>
858 <conditional name="output_format">
859 <when value="rtable">
860 <action type="format">
861 <option type="from_param" name="output_format" />
862 </action>
863 </when>
864 <when value="csv">
865 <action type="format">
866 <option type="from_param" name="output_format" />
867 </action>
868 </when>
869 </conditional>
870 </actions>
871 </data>
872 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" >
873 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
874 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
875 <actions>
876 <conditional name="output_format">
877 <when value="rtable">
878 <action type="format">
879 <option type="from_param" name="output_format" />
880 </action>
881 </when>
882 <when value="csv">
883 <action type="format">
884 <option type="from_param" name="output_format" />
885 </action>
886 </when>
887 </conditional>
888 </actions>
889 </data>
890 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" >
891 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
892 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
893 <actions>
894 <conditional name="output_format">
895 <when value="rtable">
896 <action type="format">
897 <option type="from_param" name="output_format" />
898 </action>
899 </when>
900 <when value="csv">
901 <action type="format">
902 <option type="from_param" name="output_format" />
903 </action>
904 </when>
905 </conditional>
906 </actions>
907 </data>
908 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" >
909 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
910 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
911 <filter>'library' in partition_type</filter>
912 <actions>
913 <conditional name="output_format">
914 <when value="rtable">
915 <action type="format">
916 <option type="from_param" name="output_format" />
917 </action>
918 </when>
919 <when value="csv">
920 <action type="format">
921 <option type="from_param" name="output_format" />
922 </action>
923 </when>
924 </conditional>
925 </actions>
926 </data>
927 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" >
928 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
929 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
930 <filter>'library' in partition_type</filter>
931 <actions>
932 <conditional name="output_format">
933 <when value="rtable">
934 <action type="format">
935 <option type="from_param" name="output_format" />
936 </action>
937 </when>
938 <when value="csv">
939 <action type="format">
940 <option type="from_param" name="output_format" />
941 </action>
942 </when>
943 </conditional>
944 </actions>
945 </data>
946
947 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
948 </outputs>
949 <trackster_conf/>
950 <tests>
951 <test>
952 <param name="reference_source_selector" value="history" />
953 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
954 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
955 <param name="input_calculate_coverage_over_genes" />
956 <param name="partition_type" value="sample" />
957 <param name="summary_coverage_threshold_group" value="0" />
958 <param name="output_format" value="rtable" />
959 <param name="gatk_param_type_selector" value="basic" />
960 <param name="analysis_param_type_selector" value="basic" />
961 <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" />
962 <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" />
963 <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" />
964 <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" />
965 <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" />
966 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" />
967 </test>
968 </tests>
969 <help>
970 **What it does**
971
972 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.
973
974 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;`_.
975
976 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;`_.
977
978 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions&gt;`_.
979
980 ------
981
982 **Inputs**
983
984 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.
985
986
987 **Outputs**
988
989 The output is in various table formats.
990
991
992 Go `here &lt;http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK&gt;`_ for details on GATK file formats.
993
994 -------
995
996 **Settings**::
997
998 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
999 ignoreDeletionSites boolean false Ignore sites consisting only of deletions
1000 includeDeletions boolean false Include information on deletions
1001 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
1002 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
1003 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
1004 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
1005 nBins int 499 Number of bins to use for granular binning
1006 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
1007 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
1008 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
1009 omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
1010 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
1011 partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
1012 printBaseCounts boolean false Will add base counts to per-locus output.
1013 printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
1014 start int 1 Starting (left endpoint) for granular binning
1015 stop int 500 Ending (right endpoint) for granular binning
1016 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
1017
1018 ------
1019
1020 **Citation**
1021
1022 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_
1023
1024 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
1025
1026 </help>
1027 </tool>