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comparison print_reads.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_print_reads" name="Print Reads" 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 "${output_log}"
10 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
11 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
12 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
13 #end if
14 -p 'java
15 -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
16 -T "PrintReads"
17 -o "${output_bam}"
18 \$GATK2_SITE_OPTIONS
19 ##-et "NO_ET" -K "/data/galaxy/appList/GenomeAnalysisTK-2.0-36-gf5c1c1a/gatk2_key_file" ##ET no phone home
20 ##--num_threads 4 ##not supported yet
21 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
22 #if $reference_source.reference_source_selector != "history":
23 -R "${reference_source.ref_file.fields.path}"
24 #end if
25 --BQSR "${input_recal}"
26 --disable_bam_indexing
27 '
28 ##start standard gatk options
29 #if $gatk_param_type.gatk_param_type_selector == "advanced":
30 #for $pedigree in $gatk_param_type.pedigree:
31 -p '--pedigree "${pedigree.pedigree_file}"'
32 #end for
33 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
34 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
35 #end for
36 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
37 #for $read_filter in $gatk_param_type.read_filter:
38 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
39 ###raise Exception( str( dir( $read_filter ) ) )
40 #for $name, $param in $read_filter.read_filter_type.iteritems():
41 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
42 #if hasattr( $param.input, 'truevalue' ):
43 ${param}
44 #else:
45 --${name} "${param}"
46 #end if
47 #end if
48 #end for
49 '
50 #end for
51 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
52 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
53 #end for
54
55 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
56 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
57 #end for
58
59 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
60
61 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
62 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
63 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
64 #end if
65 -p '
66 --baq "${gatk_param_type.baq}"
67 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
68 ${gatk_param_type.use_original_qualities}
69 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
70 --validation_strictness "${gatk_param_type.validation_strictness}"
71 --interval_merging "${gatk_param_type.interval_merging}"
72 ${gatk_param_type.disable_experimental_low_memory_sharding}
73 ${gatk_param_type.non_deterministic_random_seed}
74 '
75 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
76 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
77 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
78 #else
79 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
80 #end if
81 #end for
82 #end if
83
84 #if str( $reference_source.reference_source_selector ) == "history":
85 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
86 #end if
87 ##end standard gatk options
88
89 ##start analysis specific options
90 #if $analysis_param_type.analysis_param_type_selector == "advanced":
91 -p '
92 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
93 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
94 #end if
95 #if str( $analysis_param_type.default_platform ) != "default":
96 --default_platform "${analysis_param_type.default_platform}"
97 #end if
98 #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
99 --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
100 #end if
101 #if str( $analysis_param_type.force_platform ) != "default":
102 --force_platform "${analysis_param_type.force_platform}"
103 #end if
104 ${analysis_param_type.exception_if_no_tile}
105 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
106 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
107 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
108 #end if
109 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
110 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
111 #end if
112 #end if
113 ${analysis_param_type.simplify_bam}
114 --preserve_qscores_less_than "${analysis_param_type.preserve_qscores_less_than}"
115 --smoothing "${analysis_param_type.smoothing}"
116 --max_quality_score "${analysis_param_type.max_quality_score}"
117 --window_size_nqs "${analysis_param_type.window_size_nqs}"
118 --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
119 ${analysis_param_type.do_not_write_original_quals}
120 '
121 #end if
122 </command>
123 <inputs>
124 <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-BQSR,--BQSR &amp;lt;recal_file&amp;gt;" />
125 <conditional name="reference_source">
126 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
127 <option value="cached">Locally cached</option>
128 <option value="history">History</option>
129 </param>
130 <when value="cached">
131 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
132 <validator type="unspecified_build" />
133 <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 -->
134 </param>
135 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
136 <options from_data_table="gatk2_picard_indexes">
137 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
138 </options>
139 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
140 </param>
141 </when>
142 <when value="history">
143 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;" />
144 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
145 <options>
146 <filter type="data_meta" key="dbkey" ref="input_bam" />
147 </options>
148 </param>
149 </when>
150 </conditional>
151
152 <conditional name="gatk_param_type">
153 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
154 <option value="basic" selected="True">Basic</option>
155 <option value="advanced">Advanced</option>
156 </param>
157 <when value="basic">
158 <!-- Do nothing here -->
159 </when>
160 <when value="advanced">
161 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
162 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
163 </repeat>
164 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
165 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
166 </repeat>
167 <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;">
168 <option value="STRICT" selected="True">STRICT</option>
169 <option value="SILENT">SILENT</option>
170 </param>
171 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
172 <conditional name="read_filter_type">
173 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
174 <option value="BadCigar">BadCigar</option>
175 <option value="BadMate">BadMate</option>
176 <option value="DuplicateRead">DuplicateRead</option>
177 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
178 <option value="MalformedRead">MalformedRead</option>
179 <option value="MappingQuality">MappingQuality</option>
180 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
181 <option value="MappingQualityZero">MappingQualityZero</option>
182 <option value="MateSameStrand">MateSameStrand</option>
183 <option value="MaxInsertSize">MaxInsertSize</option>
184 <option value="MaxReadLength" selected="True">MaxReadLength</option>
185 <option value="MissingReadGroup">MissingReadGroup</option>
186 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
187 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
188 <option value="Platform454">Platform454</option>
189 <option value="Platform">Platform</option>
190 <option value="PlatformUnit">PlatformUnit</option>
191 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
192 <option value="ReadName">ReadName</option>
193 <option value="ReadStrand">ReadStrand</option>
194 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
195 <option value="Sample">Sample</option>
196 <option value="SingleReadGroup">SingleReadGroup</option>
197 <option value="UnmappedRead">UnmappedRead</option>
198 </param>
199 <when value="BadCigar">
200 <!-- no extra options -->
201 </when>
202 <when value="BadMate">
203 <!-- no extra options -->
204 </when>
205 <when value="DuplicateRead">
206 <!-- no extra options -->
207 </when>
208 <when value="FailsVendorQualityCheck">
209 <!-- no extra options -->
210 </when>
211 <when value="MalformedRead">
212 <!-- no extra options -->
213 </when>
214 <when value="MappingQuality">
215 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
216 </when>
217 <when value="MappingQualityUnavailable">
218 <!-- no extra options -->
219 </when>
220 <when value="MappingQualityZero">
221 <!-- no extra options -->
222 </when>
223 <when value="MateSameStrand">
224 <!-- no extra options -->
225 </when>
226 <when value="MaxInsertSize">
227 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
228 </when>
229 <when value="MaxReadLength">
230 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
231 </when>
232 <when value="MissingReadGroup">
233 <!-- no extra options -->
234 </when>
235 <when value="NoOriginalQualityScores">
236 <!-- no extra options -->
237 </when>
238 <when value="NotPrimaryAlignment">
239 <!-- no extra options -->
240 </when>
241 <when value="Platform454">
242 <!-- no extra options -->
243 </when>
244 <when value="Platform">
245 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
246 </when>
247 <when value="PlatformUnit">
248 <!-- no extra options -->
249 </when>
250 <when value="ReadGroupBlackList">
251 <!-- no extra options -->
252 </when>
253 <when value="ReadName">
254 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
255 </when>
256 <when value="ReadStrand">
257 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
258 </when>
259 <when value="ReassignMappingQuality">
260 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
261 </when>
262 <when value="Sample">
263 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
264 </when>
265 <when value="SingleReadGroup">
266 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
267 </when>
268 <when value="UnmappedRead">
269 <!-- no extra options -->
270 </when>
271 </conditional>
272 </repeat>
273 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
274 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
275 </repeat>
276 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
277 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
278 </repeat>
279
280 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
281 <option value="UNION" selected="True">UNION</option>
282 <option value="INTERSECTION">INTERSECTION</option>
283 </param>
284
285 <conditional name="downsampling_type">
286 <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;">
287 <option value="NONE" selected="True">NONE</option>
288 <option value="ALL_READS">ALL_READS</option>
289 <option value="BY_SAMPLE">BY_SAMPLE</option>
290 </param>
291 <when value="NONE">
292 <!-- no more options here -->
293 </when>
294 <when value="ALL_READS">
295 <conditional name="downsample_to_type">
296 <param name="downsample_to_type_selector" type="select" label="Downsample method">
297 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
298 <option value="downsample_to_coverage">Downsample by Coverage</option>
299 </param>
300 <when value="downsample_to_fraction">
301 <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;"/>
302 </when>
303 <when value="downsample_to_coverage">
304 <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;"/>
305 </when>
306 </conditional>
307 </when>
308 <when value="BY_SAMPLE">
309 <conditional name="downsample_to_type">
310 <param name="downsample_to_type_selector" type="select" label="Downsample method">
311 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
312 <option value="downsample_to_coverage">Downsample by Coverage</option>
313 </param>
314 <when value="downsample_to_fraction">
315 <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;"/>
316 </when>
317 <when value="downsample_to_coverage">
318 <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;"/>
319 </when>
320 </conditional>
321 </when>
322 </conditional>
323 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
324 <option value="OFF" selected="True">OFF</option>
325 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
326 <option value="RECALCULATE">RECALCULATE</option>
327 </param>
328 <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;" />
329 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
330 <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;"/>
331 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
332 <option value="STRICT" selected="True">STRICT</option>
333 <option value="LENIENT">LENIENT</option>
334 <option value="SILENT">SILENT</option>
335 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
336 </param>
337 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
338 <option value="ALL" selected="True">ALL</option>
339 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
340 </param>
341
342 <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;">
343 <conditional name="read_group_black_list_type">
344 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
345 <option value="file" selected="True">Filters in file</option>
346 <option value="text">Specify filters as a string</option>
347 </param>
348 <when value="file">
349 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
350 </when>
351 <when value="text">
352 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
353 </when>
354 </conditional>
355 </repeat>
356
357 <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"/>
358 <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"/>
359
360 </when>
361 </conditional>
362
363
364 <conditional name="analysis_param_type">
365 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
366 <option value="basic" selected="True">Basic</option>
367 <option value="advanced">Advanced</option>
368 </param>
369 <when value="basic">
370 <!-- Do nothing here -->
371 </when>
372 <when value="advanced">
373 <conditional name="default_read_group_type">
374 <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
375 <option value="default" selected="True">Don't Set</option>
376 <option value="set">Set</option>
377 </param>
378 <when value="default">
379 <!-- do nothing here -->
380 </when>
381 <when value="set">
382 <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
383 </when>
384 </conditional>
385 <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
386 <option value="default" selected="True">Don't Set</option>
387 <option value="illumina">illumina</option>
388 <option value="454">454</option>
389 <option value="solid">solid</option>
390 </param>
391 <conditional name="force_read_group_type">
392 <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
393 <option value="default" selected="True">Don't Force</option>
394 <option value="set">Force</option>
395 </param>
396 <when value="default">
397 <!-- do nothing here -->
398 </when>
399 <when value="set">
400 <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
401 </when>
402 </conditional>
403 <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
404 <option value="default" selected="True">Don't Force</option>
405 <option value="illumina">illumina</option>
406 <option value="454">454</option>
407 <option value="solid">solid</option>
408 </param>
409 <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
410 <conditional name="solid_options_type">
411 <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
412 <option value="default" selected="True">Don't Set</option>
413 <option value="set">Set</option>
414 </param>
415 <when value="default">
416 <!-- do nothing here -->
417 </when>
418 <when value="set">
419 <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
420 <option value="default" selected="True">Don't set</option>
421 <option value="DO_NOTHING">DO_NOTHING</option>
422 <option value="SET_Q_ZERO">SET_Q_ZERO</option>
423 <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
424 <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
425 </param>
426 <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
427 <option value="default" selected="True">Don't set</option>
428 <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
429 <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
430 <option value="PURGE_READ">PURGE_READ</option>
431 </param>
432 </when>
433 </conditional>
434 <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
435 <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/>
436 <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
437 <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated" help="-pQ,--preserve_qscores_less_than &amp;lt;preserve_qscores_less_than&amp;gt;"/>
438 <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &amp;lt;smoothing&amp;gt;"/>
439 <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
440 <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/>
441 </when>
442 </conditional>
443 </inputs>
444 <outputs>
445 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
446 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
447 </outputs>
448 <tests>
449 <test>
450 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
451 <param name="reference_source_selector" value="history" />
452 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
453 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
454 <param name="gatk_param_type_selector" value="basic" />
455 <param name="analysis_param_type_selector" value="basic" />
456 <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="4" />
457 <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" />
458 </test>
459 </tests>
460 <help>
461 **What it does**
462
463 This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads. Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker.
464
465 For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.html&gt;`_.
466
467 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;`_.
468
469 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
470
471 ------
472
473 **Inputs**
474
475 GenomeAnalysisTK: PrintReads accepts an aligned BAM and a recalibration CSV input files.
476
477
478 **Outputs**
479
480 The output is in BAM format.
481
482
483 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
484
485 -------
486
487 **Settings**::
488
489 default_read_group If a read has no read group then default to the provided String.
490 default_platform If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.
491 force_read_group If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.
492 force_platform If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.
493 window_size_nqs The window size used by MinimumNQSCovariate for its calculation
494 homopolymer_nback The number of previous bases to look at in HomopolymerCovariate
495 exception_if_no_tile If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
496 solid_recal_mode How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
497 solid_nocall_strategy Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
498 recal_file Filename for the input covariates table recalibration .csv file
499 out The output BAM file
500 bam_compression Compression level to use for writing BAM files
501 disable_bam_indexing Turn off on-the-fly creation of indices for output BAM files.
502 simplifyBAM If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier
503 preserve_qscores_less_than Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below &lt; 5, since base callers use these values to indicate random or bad bases
504 smoothing Number of imaginary counts to add to each bin bin order to smooth out bins with few data points, default=1
505 max_quality_score The integer value at which to cap the quality scores, default=50
506 doNotWriteOriginalQuals If true, we will not write the original quality (OQ) tag for each read
507
508 ------
509
510 **Citation**
511
512 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;`_
513
514 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;`_
515
516 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;`_
517
518 </help>
519 </tool>