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comparison depth_of_coverage.xml @ 0:74c05070a3f8 draft

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author jjohnson
date Thu, 01 Nov 2012 13:53:22 -0400
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-1:000000000000 0:74c05070a3f8
1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.4">
2 <description>on BAM files</description>
3 <requirements>
4 <requirement type="package" version="2.2">gatk</requirement>
5 <requirement type="package" version="0.1.18">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 "\$GATK2_PATH/GenomeAnalysisTK.jar"
18 -T "DepthOfCoverage"
19 \$GATK2_SITE_OPTIONS
20 ##--num_threads 4 ##hard coded, for now
21
22 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
23 #if $reference_source.reference_source_selector != "history":
24 -R "${reference_source.ref_file.fields.path}"
25 #end if
26 #if str( $input_calculate_coverage_over_genes ) != "None":
27 --calculateCoverageOverGenes "${input_calculate_coverage_over_genes}"
28 #end if
29 #if str( $partition_type ) != "None":
30 #for $pt in str( $partition_type ).split( ',' ):
31 --partitionType "${pt}"
32 #end for
33 #end if
34 --out "${output_per_locus_coverage}"
35
36 #for $ct_group in $summary_coverage_threshold_group:
37 --summaryCoverageThreshold "${ct_group.summary_coverage_threshold}"
38 #end for
39 --outputFormat "${output_format}"
40 '
41
42 ##start standard gatk options
43 #if $gatk_param_type.gatk_param_type_selector == "advanced":
44 #for $pedigree in $gatk_param_type.pedigree:
45 -p '--pedigree "${pedigree.pedigree_file}"'
46 #end for
47 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
48 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
49 #end for
50 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
51 #for $read_filter in $gatk_param_type.read_filter:
52 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
53 ###raise Exception( str( dir( $read_filter ) ) )
54 #for $name, $param in $read_filter.read_filter_type.iteritems():
55 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
56 #if hasattr( $param.input, 'truevalue' ):
57 ${param}
58 #else:
59 --${name} "${param}"
60 #end if
61 #end if
62 #end for
63 '
64 #end for
65 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
66 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
67 #end for
68
69 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
70 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
71 #end for
72
73 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
74
75 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
76 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
77 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
78 #end if
79 -p '
80 --baq "${gatk_param_type.baq}"
81 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
82 ${gatk_param_type.use_original_qualities}
83 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
84 --validation_strictness "${gatk_param_type.validation_strictness}"
85 --interval_merging "${gatk_param_type.interval_merging}"
86 ${gatk_param_type.disable_experimental_low_memory_sharding}
87 ${gatk_param_type.non_deterministic_random_seed}
88 '
89 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
90 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
91 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
92 #else
93 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
94 #end if
95 #end for
96 #end if
97
98 #if $reference_source.reference_source_selector == "history":
99 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
100 #end if
101 ##end standard gatk options
102 ##start analysis specific options
103 #if $analysis_param_type.analysis_param_type_selector == "advanced":
104 -p '
105 ${analysis_param_type.ignore_deletion_sites}
106 ${analysis_param_type.include_deletions}
107 --maxBaseQuality "${analysis_param_type.max_base_quality}"
108 --maxMappingQuality "${analysis_param_type.max_mapping_quality}"
109 --minBaseQuality "${analysis_param_type.min_base_quality}"
110 --minMappingQuality "${analysis_param_type.min_mapping_quality}"
111 --nBins "${analysis_param_type.n_bins}"
112 ${analysis_param_type.omit_depth_output_at_each_base}
113 ${analysis_param_type.omit_interval_statistics}
114 ${analysis_param_type.omit_locus_table}
115 ${analysis_param_type.omit_per_sample_stats}
116 ${analysis_param_type.print_base_counts}
117 ${analysis_param_type.print_bin_endpoints_and_exit}
118 --start "${analysis_param_type.start}"
119 --stop "${analysis_param_type.stop}"
120 '
121 #end if
122 ##Move additional files to final location
123 #if str( $partition_type ) != "None":
124 #set $partition_types = str( $partition_type ).split( ',' )
125 #else:
126 #set $partition_types = [ 'sample' ]
127 #end if
128 #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 ) == "" ):
129 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
130 &amp;&amp; mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample}
131 &amp;&amp; mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample}
132 #end if
133 #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 ) == "" ):
134 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample}
135 &amp;&amp; mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample}
136 #end if
137 #if str( $input_calculate_coverage_over_genes ) != "None":
138 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_summary ${output_gene_summary_sample}
139 &amp;&amp; mv ${output_per_locus_coverage}.sample_gene_statistics ${output_gene_statistics_sample}
140 #end if
141 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
142 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_counts ${output_cumulative_coverage_counts_sample}
143 &amp;&amp; mv ${output_per_locus_coverage}.sample_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_sample}
144 #end if
145 #end if
146
147 #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 ) == "" ):
148 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
149 &amp;&amp; mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup}
150 &amp;&amp; mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup}
151 #end if
152 #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 ) == "" ):
153 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup}
154 &amp;&amp; mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup}
155 #end if
156 #if str( $input_calculate_coverage_over_genes ) != "None":
157 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_summary ${output_gene_summary_readgroup}
158 &amp;&amp; mv ${output_per_locus_coverage}.read_group_gene_statistics ${output_gene_statistics_readgroup}
159 #end if
160 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
161 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_counts ${output_cumulative_coverage_counts_readgroup}
162 &amp;&amp; mv ${output_per_locus_coverage}.read_group_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_readgroup}
163 #end if
164 #end if
165
166 #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 ) == "" ):
167 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_per_sample_stats ) == "":
168 &amp;&amp; mv ${output_per_locus_coverage}.library_summary ${output_summary_library}
169 &amp;&amp; mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library}
170 #end if
171 #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 ) == "" ):
172 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library}
173 &amp;&amp; mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library}
174 #end if
175 #if str( $input_calculate_coverage_over_genes ) != "None":
176 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_summary ${output_gene_summary_library}
177 &amp;&amp; mv ${output_per_locus_coverage}.library_gene_statistics ${output_gene_statistics_library}
178 #end if
179 #if str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_depth_output_at_each_base ) == "":
180 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_counts ${output_cumulative_coverage_counts_library}
181 &amp;&amp; mv ${output_per_locus_coverage}.library_cumulative_coverage_proportions ${output_cumulative_coverage_proportions_library}
182 #end if
183 #end if
184
185
186 </command>
187 <inputs>
188 <conditional name="reference_source">
189 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
190 <option value="cached">Locally cached</option>
191 <option value="history">History</option>
192 </param>
193 <when value="cached">
194 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
195 <param name="input_bam" type="data" format="bam" label="BAM file">
196 <validator type="unspecified_build" />
197 <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 -->
198 </param>
199 </repeat>
200 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
201 <options from_data_table="gatk2_picard_indexes">
202 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
203 </options>
204 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
205 </param>
206 </when>
207 <when value="history"> <!-- FIX ME!!!! -->
208 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
209 <param name="input_bam" type="data" format="bam" label="BAM file" />
210 </repeat>
211 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
212 </when>
213 </conditional>
214
215 <param name="input_calculate_coverage_over_genes" type="data" format="data" label="RefSeq Rod" optional="True" help="-geneList,--calculateCoverageOverGenes &amp;lt;calculateCoverageOverGenes&amp;gt;" />
216
217 <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;">
218 <option value="sample" selected="True">sample</option>
219 <option value="readgroup">readgroup</option>
220 <option value="library">library</option>
221 </param>
222
223 <repeat name="summary_coverage_threshold_group" title="Summary coverage threshold" help="-ct,--summaryCoverageThreshold &amp;lt;summaryCoverageThreshold&amp;gt;">
224 <param name="summary_coverage_threshold" type="integer" value="15" label="for summary file outputs, report the % of bases covered to &gt;= this number" />
225 </repeat>
226
227 <param name="output_format" type="select" label="Output format" help="--outputFormat &amp;lt;outputFormat&amp;gt;" >
228 <option value="csv">csv</option>
229 <option value="table">table</option>
230 <option value="rtable" selected="True">rtable</option>
231 </param>
232
233 <conditional name="gatk_param_type">
234 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
235 <option value="basic" selected="True">Basic</option>
236 <option value="advanced">Advanced</option>
237 </param>
238 <when value="basic">
239 <!-- Do nothing here -->
240 </when>
241 <when value="advanced">
242 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
243 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
244 </repeat>
245 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
246 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
247 </repeat>
248 <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;">
249 <option value="STRICT" selected="True">STRICT</option>
250 <option value="SILENT">SILENT</option>
251 </param>
252 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
253 <conditional name="read_filter_type">
254 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
255 <option value="BadCigar">BadCigar</option>
256 <option value="BadMate">BadMate</option>
257 <option value="DuplicateRead">DuplicateRead</option>
258 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
259 <option value="MalformedRead">MalformedRead</option>
260 <option value="MappingQuality">MappingQuality</option>
261 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
262 <option value="MappingQualityZero">MappingQualityZero</option>
263 <option value="MateSameStrand">MateSameStrand</option>
264 <option value="MaxInsertSize">MaxInsertSize</option>
265 <option value="MaxReadLength" selected="True">MaxReadLength</option>
266 <option value="MissingReadGroup">MissingReadGroup</option>
267 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
268 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
269 <option value="Platform454">Platform454</option>
270 <option value="Platform">Platform</option>
271 <option value="PlatformUnit">PlatformUnit</option>
272 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
273 <option value="ReadName">ReadName</option>
274 <option value="ReadStrand">ReadStrand</option>
275 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
276 <option value="Sample">Sample</option>
277 <option value="SingleReadGroup">SingleReadGroup</option>
278 <option value="UnmappedRead">UnmappedRead</option>
279 </param>
280 <when value="BadCigar">
281 <!-- no extra options -->
282 </when>
283 <when value="BadMate">
284 <!-- no extra options -->
285 </when>
286 <when value="DuplicateRead">
287 <!-- no extra options -->
288 </when>
289 <when value="FailsVendorQualityCheck">
290 <!-- no extra options -->
291 </when>
292 <when value="MalformedRead">
293 <!-- no extra options -->
294 </when>
295 <when value="MappingQuality">
296 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
297 </when>
298 <when value="MappingQualityUnavailable">
299 <!-- no extra options -->
300 </when>
301 <when value="MappingQualityZero">
302 <!-- no extra options -->
303 </when>
304 <when value="MateSameStrand">
305 <!-- no extra options -->
306 </when>
307 <when value="MaxInsertSize">
308 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
309 </when>
310 <when value="MaxReadLength">
311 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
312 </when>
313 <when value="MissingReadGroup">
314 <!-- no extra options -->
315 </when>
316 <when value="NoOriginalQualityScores">
317 <!-- no extra options -->
318 </when>
319 <when value="NotPrimaryAlignment">
320 <!-- no extra options -->
321 </when>
322 <when value="Platform454">
323 <!-- no extra options -->
324 </when>
325 <when value="Platform">
326 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
327 </when>
328 <when value="PlatformUnit">
329 <!-- no extra options -->
330 </when>
331 <when value="ReadGroupBlackList">
332 <!-- no extra options -->
333 </when>
334 <when value="ReadName">
335 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
336 </when>
337 <when value="ReadStrand">
338 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
339 </when>
340 <when value="ReassignMappingQuality">
341 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
342 </when>
343 <when value="Sample">
344 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
345 </when>
346 <when value="SingleReadGroup">
347 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
348 </when>
349 <when value="UnmappedRead">
350 <!-- no extra options -->
351 </when>
352 </conditional>
353 </repeat>
354 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
355 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
356 </repeat>
357 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
358 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
359 </repeat>
360
361 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
362 <option value="UNION" selected="True">UNION</option>
363 <option value="INTERSECTION">INTERSECTION</option>
364 </param>
365
366 <conditional name="downsampling_type">
367 <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;">
368 <option value="NONE" selected="True">NONE</option>
369 <option value="ALL_READS">ALL_READS</option>
370 <option value="BY_SAMPLE">BY_SAMPLE</option>
371 </param>
372 <when value="NONE">
373 <!-- no more options here -->
374 </when>
375 <when value="ALL_READS">
376 <conditional name="downsample_to_type">
377 <param name="downsample_to_type_selector" type="select" label="Downsample method">
378 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
379 <option value="downsample_to_coverage">Downsample by Coverage</option>
380 </param>
381 <when value="downsample_to_fraction">
382 <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;"/>
383 </when>
384 <when value="downsample_to_coverage">
385 <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;"/>
386 </when>
387 </conditional>
388 </when>
389 <when value="BY_SAMPLE">
390 <conditional name="downsample_to_type">
391 <param name="downsample_to_type_selector" type="select" label="Downsample method">
392 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
393 <option value="downsample_to_coverage">Downsample by Coverage</option>
394 </param>
395 <when value="downsample_to_fraction">
396 <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;"/>
397 </when>
398 <when value="downsample_to_coverage">
399 <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;"/>
400 </when>
401 </conditional>
402 </when>
403 </conditional>
404 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
405 <option value="OFF" selected="True">OFF</option>
406 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
407 <option value="RECALCULATE">RECALCULATE</option>
408 </param>
409 <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;" />
410 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
411 <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;"/>
412 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
413 <option value="STRICT" selected="True">STRICT</option>
414 <option value="LENIENT">LENIENT</option>
415 <option value="SILENT">SILENT</option>
416 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
417 </param>
418 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
419 <option value="ALL" selected="True">ALL</option>
420 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
421 </param>
422
423 <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;">
424 <conditional name="read_group_black_list_type">
425 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
426 <option value="file" selected="True">Filters in file</option>
427 <option value="text">Specify filters as a string</option>
428 </param>
429 <when value="file">
430 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
431 </when>
432 <when value="text">
433 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
434 </when>
435 </conditional>
436 </repeat>
437
438 <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"/>
439 <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"/>
440
441 </when>
442 </conditional>
443
444 <conditional name="analysis_param_type">
445 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
446 <option value="basic" selected="True">Basic</option>
447 <option value="advanced">Advanced</option>
448 </param>
449 <when value="basic">
450 <!-- Do nothing here -->
451 </when>
452 <when value="advanced">
453 <param name="ignore_deletion_sites" type="boolean" truevalue="--ignoreDeletionSites" falsevalue="" checked="False" label="Ignore sites consisting only of deletions" help="--ignoreDeletionSites" />
454 <param name="include_deletions" type="boolean" truevalue="--includeDeletions" falsevalue="" checked="False" label="Include information on deletions" help="-dels,--includeDeletions" />
455 <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;" />
456 <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;" />
457 <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;" />
458 <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;" />
459 <param name="n_bins" type="integer" value="499" label="Number of bins to use for granular binning" help="--nBins &amp;lt;nBins&amp;gt;" />
460 <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" />
461 <param name="omit_interval_statistics" type="boolean" truevalue="--omitIntervalStatistics" falsevalue="" checked="False" label="Omit the per-interval statistics section" help="-omitIntervals,--omitIntervalStatistics" />
462 <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" />
463 <param name="omit_per_sample_stats" type="boolean" truevalue="--omitPerSampleStats" falsevalue="" checked="False" label="Omit the summary files per-sample." help="-omitSampleSummary,--omitPerSampleStats" />
464 <param name="print_base_counts" type="boolean" truevalue="--printBaseCounts" falsevalue="" checked="False" label="Add base counts to per-locus output" help="-baseCounts,--printBaseCounts" />
465 <param name="print_bin_endpoints_and_exit" type="boolean" truevalue="--printBinEndpointsAndExit" falsevalue="" checked="False" label="Print the bin values and exits immediately" help="--printBinEndpointsAndExit" />
466 <param name="start" type="integer" value="1" label="Starting (left endpoint) for granular binning" help="--start &amp;lt;start&amp;gt;" />
467 <param name="stop" type="integer" value="500" label="Ending (right endpoint) for granular binning" help="--stop &amp;lt;stop&amp;gt;" />
468 </when>
469 </conditional>
470 </inputs>
471 <outputs>
472 <data format="tabular" name="output_per_locus_coverage" label="${tool.name} on ${on_string} (per locus coverage)" >
473 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
474 <actions>
475 <conditional name="output_format">
476 <when value="rtable">
477 <action type="format">
478 <option type="from_param" name="output_format" />
479 </action>
480 </when>
481 <when value="csv">
482 <action type="format">
483 <option type="from_param" name="output_format" />
484 </action>
485 </when>
486 </conditional>
487 </actions>
488 </data>
489 <data format="tabular" name="output_summary_sample" label="${tool.name} on ${on_string} (output summary sample)" >
490 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
491 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
492 <filter>'sample' in partition_type or not partition_type</filter>
493 <actions>
494 <conditional name="output_format">
495 <when value="rtable">
496 <action type="format">
497 <option type="from_param" name="output_format" />
498 </action>
499 </when>
500 <when value="csv">
501 <action type="format">
502 <option type="from_param" name="output_format" />
503 </action>
504 </when>
505 </conditional>
506 </actions>
507 </data>
508 <data format="tabular" name="output_statistics_sample" label="${tool.name} on ${on_string} (output statistics sample)" >
509 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
510 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
511 <filter>'sample' in partition_type or not partition_type</filter>
512 <actions>
513 <conditional name="output_format">
514 <when value="rtable">
515 <action type="format">
516 <option type="from_param" name="output_format" />
517 </action>
518 </when>
519 <when value="csv">
520 <action type="format">
521 <option type="from_param" name="output_format" />
522 </action>
523 </when>
524 </conditional>
525 </actions>
526 </data>
527 <data format="tabular" name="output_interval_summary_sample" label="${tool.name} on ${on_string} (output interval summary sample)" >
528 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
529 <filter>'sample' in partition_type or not partition_type</filter>
530 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
531 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
532 <actions>
533 <conditional name="output_format">
534 <when value="rtable">
535 <action type="format">
536 <option type="from_param" name="output_format" />
537 </action>
538 </when>
539 <when value="csv">
540 <action type="format">
541 <option type="from_param" name="output_format" />
542 </action>
543 </when>
544 </conditional>
545 </actions>
546 </data>
547 <data format="tabular" name="output_interval_statistics_sample" label="${tool.name} on ${on_string} (output interval statistics sample)" >
548 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
549 <filter>'sample' in partition_type or not partition_type</filter>
550 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
551 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
552 <actions>
553 <conditional name="output_format">
554 <when value="rtable">
555 <action type="format">
556 <option type="from_param" name="output_format" />
557 </action>
558 </when>
559 <when value="csv">
560 <action type="format">
561 <option type="from_param" name="output_format" />
562 </action>
563 </when>
564 </conditional>
565 </actions>
566 </data>
567 <data format="tabular" name="output_gene_summary_sample" label="${tool.name} on ${on_string} (output gene summary sample)" >
568 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
569 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
570 <actions>
571 <conditional name="output_format">
572 <when value="rtable">
573 <action type="format">
574 <option type="from_param" name="output_format" />
575 </action>
576 </when>
577 <when value="csv">
578 <action type="format">
579 <option type="from_param" name="output_format" />
580 </action>
581 </when>
582 </conditional>
583 </actions>
584 </data>
585 <data format="tabular" name="output_gene_statistics_sample" label="${tool.name} on ${on_string} (output gene statistics sample)" >
586 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
587 <filter>input_calculate_coverage_over_genes is not None and 'sample' in partition_type or not partition_type</filter>
588 <actions>
589 <conditional name="output_format">
590 <when value="rtable">
591 <action type="format">
592 <option type="from_param" name="output_format" />
593 </action>
594 </when>
595 <when value="csv">
596 <action type="format">
597 <option type="from_param" name="output_format" />
598 </action>
599 </when>
600 </conditional>
601 </actions>
602 </data>
603 <data format="tabular" name="output_cumulative_coverage_counts_sample" label="${tool.name} on ${on_string} (output cumulative coverage counts sample)" >
604 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
605 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
606 <filter>'sample' in partition_type or not partition_type</filter>
607 <actions>
608 <conditional name="output_format">
609 <when value="rtable">
610 <action type="format">
611 <option type="from_param" name="output_format" />
612 </action>
613 </when>
614 <when value="csv">
615 <action type="format">
616 <option type="from_param" name="output_format" />
617 </action>
618 </when>
619 </conditional>
620 </actions>
621 </data>
622 <data format="tabular" name="output_cumulative_coverage_proportions_sample" label="${tool.name} on ${on_string} (output cumulative coverage proportions sample)" >
623 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
624 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
625 <filter>'sample' in partition_type or not partition_type</filter>
626 <actions>
627 <conditional name="output_format">
628 <when value="rtable">
629 <action type="format">
630 <option type="from_param" name="output_format" />
631 </action>
632 </when>
633 <when value="csv">
634 <action type="format">
635 <option type="from_param" name="output_format" />
636 </action>
637 </when>
638 </conditional>
639 </actions>
640 </data>
641
642 <data format="tabular" name="output_summary_readgroup" label="${tool.name} on ${on_string} (output summary readgroup)" >
643 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
644 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
645 <filter>'readgroup' in partition_type</filter>
646 <actions>
647 <conditional name="output_format">
648 <when value="rtable">
649 <action type="format">
650 <option type="from_param" name="output_format" />
651 </action>
652 </when>
653 <when value="csv">
654 <action type="format">
655 <option type="from_param" name="output_format" />
656 </action>
657 </when>
658 </conditional>
659 </actions>
660 </data>
661 <data format="tabular" name="output_statistics_readgroup" label="${tool.name} on ${on_string} (output statistics readgroup)" >
662 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
663 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
664 <filter>'readgroup' in partition_type</filter>
665 <actions>
666 <conditional name="output_format">
667 <when value="rtable">
668 <action type="format">
669 <option type="from_param" name="output_format" />
670 </action>
671 </when>
672 <when value="csv">
673 <action type="format">
674 <option type="from_param" name="output_format" />
675 </action>
676 </when>
677 </conditional>
678 </actions>
679 </data>
680 <data format="tabular" name="output_interval_summary_readgroup" label="${tool.name} on ${on_string} (output interval summary readgroup)" >
681 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
682 <filter>'readgroup' in partition_type</filter>
683 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
684 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
685 <actions>
686 <conditional name="output_format">
687 <when value="rtable">
688 <action type="format">
689 <option type="from_param" name="output_format" />
690 </action>
691 </when>
692 <when value="csv">
693 <action type="format">
694 <option type="from_param" name="output_format" />
695 </action>
696 </when>
697 </conditional>
698 </actions>
699 </data>
700 <data format="tabular" name="output_interval_statistics_readgroup" label="${tool.name} on ${on_string} (output interval statistics readgroup)" >
701 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
702 <filter>'readgroup' in partition_type</filter>
703 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
704 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
705 <actions>
706 <conditional name="output_format">
707 <when value="rtable">
708 <action type="format">
709 <option type="from_param" name="output_format" />
710 </action>
711 </when>
712 <when value="csv">
713 <action type="format">
714 <option type="from_param" name="output_format" />
715 </action>
716 </when>
717 </conditional>
718 </actions>
719 </data>
720 <data format="tabular" name="output_gene_summary_readgroup" label="${tool.name} on ${on_string} (output gene summary readgroup)" >
721 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
722 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
723 <actions>
724 <conditional name="output_format">
725 <when value="rtable">
726 <action type="format">
727 <option type="from_param" name="output_format" />
728 </action>
729 </when>
730 <when value="csv">
731 <action type="format">
732 <option type="from_param" name="output_format" />
733 </action>
734 </when>
735 </conditional>
736 </actions>
737 </data>
738 <data format="tabular" name="output_gene_statistics_readgroup" label="${tool.name} on ${on_string} (output gene statistics readgroup)" >
739 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
740 <filter>input_calculate_coverage_over_genes is not None and 'readgroup' in partition_type or not partition_type</filter>
741 <actions>
742 <conditional name="output_format">
743 <when value="rtable">
744 <action type="format">
745 <option type="from_param" name="output_format" />
746 </action>
747 </when>
748 <when value="csv">
749 <action type="format">
750 <option type="from_param" name="output_format" />
751 </action>
752 </when>
753 </conditional>
754 </actions>
755 </data>
756 <data format="tabular" name="output_cumulative_coverage_counts_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage counts readgroup)" >
757 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
758 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
759 <filter>'readgroup' in partition_type</filter>
760 <actions>
761 <conditional name="output_format">
762 <when value="rtable">
763 <action type="format">
764 <option type="from_param" name="output_format" />
765 </action>
766 </when>
767 <when value="csv">
768 <action type="format">
769 <option type="from_param" name="output_format" />
770 </action>
771 </when>
772 </conditional>
773 </actions>
774 </data>
775 <data format="tabular" name="output_cumulative_coverage_proportions_readgroup" label="${tool.name} on ${on_string} (output cumulative coverage proportions readgroup)" >
776 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
777 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
778 <filter>'readgroup' in partition_type</filter>
779 <actions>
780 <conditional name="output_format">
781 <when value="rtable">
782 <action type="format">
783 <option type="from_param" name="output_format" />
784 </action>
785 </when>
786 <when value="csv">
787 <action type="format">
788 <option type="from_param" name="output_format" />
789 </action>
790 </when>
791 </conditional>
792 </actions>
793 </data>
794
795 <data format="tabular" name="output_summary_library" label="${tool.name} on ${on_string} (output summary library)" >
796 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
797 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
798 <filter>'library' in partition_type</filter>
799 <actions>
800 <conditional name="output_format">
801 <when value="rtable">
802 <action type="format">
803 <option type="from_param" name="output_format" />
804 </action>
805 </when>
806 <when value="csv">
807 <action type="format">
808 <option type="from_param" name="output_format" />
809 </action>
810 </when>
811 </conditional>
812 </actions>
813 </data>
814 <data format="tabular" name="output_statistics_library" label="${tool.name} on ${on_string} (output statistics library)" >
815 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_per_sample_stats'] == False</filter>
816 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
817 <filter>'library' in partition_type</filter>
818 <actions>
819 <conditional name="output_format">
820 <when value="rtable">
821 <action type="format">
822 <option type="from_param" name="output_format" />
823 </action>
824 </when>
825 <when value="csv">
826 <action type="format">
827 <option type="from_param" name="output_format" />
828 </action>
829 </when>
830 </conditional>
831 </actions>
832 </data>
833 <data format="tabular" name="output_interval_summary_library" label="${tool.name} on ${on_string} (output interval summary library)" >
834 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
835 <filter>'library' in partition_type</filter>
836 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
837 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
838 <actions>
839 <conditional name="output_format">
840 <when value="rtable">
841 <action type="format">
842 <option type="from_param" name="output_format" />
843 </action>
844 </when>
845 <when value="csv">
846 <action type="format">
847 <option type="from_param" name="output_format" />
848 </action>
849 </when>
850 </conditional>
851 </actions>
852 </data>
853 <data format="tabular" name="output_interval_statistics_library" label="${tool.name} on ${on_string} (output interval statistics library)" >
854 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
855 <filter>'library' in partition_type</filter>
856 <filter>gatk_param_type['gatk_param_type_selector'] == "advanced" and len( gatk_param_type['input_interval_repeat'] )</filter>
857 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_interval_statistics'] == False</filter>
858 <actions>
859 <conditional name="output_format">
860 <when value="rtable">
861 <action type="format">
862 <option type="from_param" name="output_format" />
863 </action>
864 </when>
865 <when value="csv">
866 <action type="format">
867 <option type="from_param" name="output_format" />
868 </action>
869 </when>
870 </conditional>
871 </actions>
872 </data>
873 <data format="tabular" name="output_gene_summary_library" label="${tool.name} on ${on_string} (output gene summary library)" >
874 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
875 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
876 <actions>
877 <conditional name="output_format">
878 <when value="rtable">
879 <action type="format">
880 <option type="from_param" name="output_format" />
881 </action>
882 </when>
883 <when value="csv">
884 <action type="format">
885 <option type="from_param" name="output_format" />
886 </action>
887 </when>
888 </conditional>
889 </actions>
890 </data>
891 <data format="tabular" name="output_gene_statistics_library" label="${tool.name} on ${on_string} (output gene statistics library)" >
892 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
893 <filter>input_calculate_coverage_over_genes is not None and 'library' in partition_type or not partition_type</filter>
894 <actions>
895 <conditional name="output_format">
896 <when value="rtable">
897 <action type="format">
898 <option type="from_param" name="output_format" />
899 </action>
900 </when>
901 <when value="csv">
902 <action type="format">
903 <option type="from_param" name="output_format" />
904 </action>
905 </when>
906 </conditional>
907 </actions>
908 </data>
909 <data format="tabular" name="output_cumulative_coverage_counts_library" label="${tool.name} on ${on_string} (output cumulative coverage counts library)" >
910 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
911 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
912 <filter>'library' in partition_type</filter>
913 <actions>
914 <conditional name="output_format">
915 <when value="rtable">
916 <action type="format">
917 <option type="from_param" name="output_format" />
918 </action>
919 </when>
920 <when value="csv">
921 <action type="format">
922 <option type="from_param" name="output_format" />
923 </action>
924 </when>
925 </conditional>
926 </actions>
927 </data>
928 <data format="tabular" name="output_cumulative_coverage_proportions_library" label="${tool.name} on ${on_string} (output cumulative coverage proportions library)" >
929 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['omit_depth_output_at_each_base'] == False</filter>
930 <filter>analysis_param_type['analysis_param_type_selector'] == "basic" or analysis_param_type['print_bin_endpoints_and_exit'] == False</filter>
931 <filter>'library' in partition_type</filter>
932 <actions>
933 <conditional name="output_format">
934 <when value="rtable">
935 <action type="format">
936 <option type="from_param" name="output_format" />
937 </action>
938 </when>
939 <when value="csv">
940 <action type="format">
941 <option type="from_param" name="output_format" />
942 </action>
943 </when>
944 </conditional>
945 </actions>
946 </data>
947
948 <data format="tabular" name="output_log" label="${tool.name} on ${on_string} (log)" />
949 </outputs>
950 <trackster_conf/>
951 <tests>
952 <test>
953 <param name="reference_source_selector" value="history" />
954 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
955 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
956 <param name="input_calculate_coverage_over_genes" />
957 <param name="partition_type" value="sample" />
958 <param name="summary_coverage_threshold_group" value="0" />
959 <param name="output_format" value="rtable" />
960 <param name="gatk_param_type_selector" value="basic" />
961 <param name="analysis_param_type_selector" value="basic" />
962 <output name="output_per_locus_coverage" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular" />
963 <output name="output_summary_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular" />
964 <output name="output_statistics_sample" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular" />
965 <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" />
966 <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" />
967 <output name="output_log" file="gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains" compare="contains" />
968 </test>
969 </tests>
970 <help>
971 **What it does**
972
973 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.
974
975 For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html&gt;`_.
976
977 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
978
979 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
980
981 ------
982
983 **Inputs**
984
985 GenomeAnalysisTK: DepthOfCoverage accepts aligned BAM input files.
986
987
988 **Outputs**
989
990 The output is in various table formats.
991
992
993 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
994
995 -------
996
997 **Settings**::
998
999 calculateCoverageOverGenes File NA Calculate the coverage statistics over this list of genes. Currently accepts RefSeq.
1000 ignoreDeletionSites boolean false Ignore sites consisting only of deletions
1001 includeDeletions boolean false Include information on deletions
1002 maxBaseQuality byte 127 Maximum quality of bases to count towards depth. Defaults to 127 (Byte.MAX_VALUE).
1003 maxMappingQuality int 2147483647 Maximum mapping quality of reads to count towards depth. Defaults to 2^31-1 (Integer.MAX_VALUE).
1004 minBaseQuality byte -1 Minimum quality of bases to count towards depth. Defaults to -1.
1005 minMappingQuality int -1 Minimum mapping quality of reads to count towards depth. Defaults to -1.
1006 nBins int 499 Number of bins to use for granular binning
1007 omitDepthOutputAtEachBase boolean false Will omit the output of the depth of coverage at each base, which should result in speedup
1008 omitIntervalStatistics boolean false Will omit the per-interval statistics section, which should result in speedup
1009 omitLocusTable boolean false Will not calculate the per-sample per-depth counts of loci, which should result in speedup
1010 omitPerSampleStats boolean false Omits the summary files per-sample. These statistics are still calculated, so this argument will not improve runtime.
1011 outputFormat String rtable the format of the output file (e.g. csv, table, rtable); defaults to r-readable table
1012 partitionType Set[Partition] [sample] Partition type for depth of coverage. Defaults to sample. Can be any combination of sample, readgroup, library.
1013 printBaseCounts boolean false Will add base counts to per-locus output.
1014 printBinEndpointsAndExit boolean false Prints the bin values and exits immediately. Use to calibrate what bins you want before running on data.
1015 start int 1 Starting (left endpoint) for granular binning
1016 stop int 500 Ending (right endpoint) for granular binning
1017 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
1018
1019 ------
1020
1021 **Citation**
1022
1023 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;`_
1024
1025 Please also site `McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297-303. Epub 2010 Jul 19. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20644199&gt;`_
1026
1027 If you use this tool in Galaxy, please cite `Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20069535&gt;`_
1028
1029 </help>
1030 </tool>