Mercurial > repos > iuc > gatk2

comparison gatk2_macros.xml @ 0:340633249b3d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Mon, 02 Dec 2013 06:18:36 -0500
parents
children 8bcc13094767
comparison
equal deleted inserted replaced
-1:000000000000 0:340633249b3d
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="0.1.19">samtools</requirement>
5 <requirement type="set_environment">GATK2_PATH</requirement>
6 <requirement type="set_environment">GATK2_SITE_OPTIONS</requirement>
7 </requirements>
8 </xml>
9 <token name="@THREADS@">
10 --num_threads \${GALAXY_SLOTS:-4}
11 </token>
12 <token name="@JAR_PATH@">
13 java -jar "\$GATK2_PATH/GenomeAnalysisTK.jar"
14 </token>
15 <template name="standard_gatk_options">
16 ##start standard gatk options
17 #if $gatk_param_type.gatk_param_type_selector == "advanced":
18 #for $pedigree in $gatk_param_type.pedigree:
19 -p '--pedigree "${pedigree.pedigree_file}"'
20 #end for
21 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
22 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
23 #end for
24 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
25 #set default_read_filters = ['MalformedRead']
26 #for $read_filter in $gatk_param_type.read_filter:
27 -p '
28 #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
29 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
30 #end if
31 #for $name, $param in $read_filter.read_filter_type.iteritems():
32 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
33 #if hasattr( $param.input, 'truevalue' ):
34 ${param}
35 #else:
36 --${name} "${param}"
37 #end if
38 #end if
39 #end for
40 '
41 #end for
42 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
43 -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
44 #end for
45
46 #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
47 -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
48 #end for
49
50 -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
51
52 -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
53 #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
54 -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
55 #end if
56 -p '
57 --baq "${gatk_param_type.baq}"
58 --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
59 ${gatk_param_type.use_original_qualities}
60 --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
61 --validation_strictness "${gatk_param_type.validation_strictness}"
62 --interval_merging "${gatk_param_type.interval_merging}"
63 ${gatk_param_type.disable_experimental_low_memory_sharding}
64 ${gatk_param_type.fix_misencoded_quality_scores}
65 ${gatk_param_type.non_deterministic_random_seed}
66 '
67 #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
68 #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
69 -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
70 #else
71 -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
72 #end if
73 #end for
74 #end if
75
76 #if str( $reference_source.reference_source_selector ) == "history":
77 -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
78 #end if
79 ##end standard gatk options
80 </template>
81 <xml name="gatk_param_type_conditional">
82 <conditional name="gatk_param_type">
83 <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
84 <option value="basic" selected="True">Basic</option>
85 <option value="advanced">Advanced</option>
86 </param>
87 <when value="basic">
88 <!-- Do nothing here -->
89 </when>
90 <when value="advanced">
91 <repeat name="pedigree" title="Pedigree file" help="-ped,--pedigree &amp;lt;pedigree&amp;gt;">
92 <param name="pedigree_file" type="data" format="txt" label="Pedigree files for samples"/>
93 </repeat>
94 <repeat name="pedigree_string_repeat" title="Pedigree string" help="-pedString,--pedigreeString &amp;lt;pedigreeString&amp;gt;">
95 <param name="pedigree_string" type="text" value="" label="Pedigree string for samples"/>
96 </repeat>
97 <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;">
98 <option value="STRICT" selected="True">STRICT</option>
99 <option value="SILENT">SILENT</option>
100 </param>
101 <repeat name="read_filter" title="Read Filter" help="-rf,--read_filter &amp;lt;read_filter&amp;gt;">
102 <conditional name="read_filter_type">
103 <param name="read_filter_type_selector" type="select" label="Read Filter Type">
104 <option value="BadCigar">BadCigar</option>
105 <option value="BadMate">BadMate</option>
106 <option value="DuplicateRead">DuplicateRead</option>
107 <option value="FailsVendorQualityCheck">FailsVendorQualityCheck</option>
108 <option value="MalformedRead">MalformedRead</option>
109 <option value="MappingQuality">MappingQuality</option>
110 <option value="MappingQualityUnavailable">MappingQualityUnavailable</option>
111 <option value="MappingQualityZero">MappingQualityZero</option>
112 <option value="MateSameStrand">MateSameStrand</option>
113 <option value="MaxInsertSize">MaxInsertSize</option>
114 <option value="MaxReadLength" selected="True">MaxReadLength</option>
115 <option value="MissingReadGroup">MissingReadGroup</option>
116 <option value="NoOriginalQualityScores">NoOriginalQualityScores</option>
117 <option value="NotPrimaryAlignment">NotPrimaryAlignment</option>
118 <option value="Platform454">Platform454</option>
119 <option value="Platform">Platform</option>
120 <option value="PlatformUnit">PlatformUnit</option>
121 <option value="ReadGroupBlackList">ReadGroupBlackList</option>
122 <option value="ReadName">ReadName</option>
123 <option value="ReadStrand">ReadStrand</option>
124 <option value="ReassignMappingQuality">ReassignMappingQuality</option>
125 <option value="Sample">Sample</option>
126 <option value="SingleReadGroup">SingleReadGroup</option>
127 <option value="UnmappedRead">UnmappedRead</option>
128 </param>
129 <when value="BadCigar">
130 <!-- no extra options -->
131 </when>
132 <when value="BadMate">
133 <!-- no extra options -->
134 </when>
135 <when value="DuplicateRead">
136 <!-- no extra options -->
137 </when>
138 <when value="FailsVendorQualityCheck">
139 <!-- no extra options -->
140 </when>
141 <when value="MalformedRead">
142 <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
143 </when>
144 <when value="MappingQuality">
145 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
146 </when>
147 <when value="MappingQualityUnavailable">
148 <!-- no extra options -->
149 </when>
150 <when value="MappingQualityZero">
151 <!-- no extra options -->
152 </when>
153 <when value="MateSameStrand">
154 <!-- no extra options -->
155 </when>
156 <when value="MaxInsertSize">
157 <param name="maxInsertSize" type="integer" value="1000000" label="Discard reads with insert size greater than the specified value"/>
158 </when>
159 <when value="MaxReadLength">
160 <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
161 </when>
162 <when value="MissingReadGroup">
163 <!-- no extra options -->
164 </when>
165 <when value="NoOriginalQualityScores">
166 <!-- no extra options -->
167 </when>
168 <when value="NotPrimaryAlignment">
169 <!-- no extra options -->
170 </when>
171 <when value="Platform454">
172 <!-- no extra options -->
173 </when>
174 <when value="Platform">
175 <param name="PLFilterName" type="text" value="" label="Discard reads with RG:PL attribute containing this string"/>
176 </when>
177 <when value="PlatformUnit">
178 <!-- no extra options -->
179 </when>
180 <when value="ReadGroupBlackList">
181 <!-- no extra options -->
182 </when>
183 <when value="ReadName">
184 <param name="readName" type="text" value="" label="Filter out all reads except those with this read name"/>
185 </when>
186 <when value="ReadStrand">
187 <param name="filterPositive" type="boolean" truevalue="--filterPositive" falsevalue="" label="Discard reads on the forward strand"/>
188 </when>
189 <when value="ReassignMappingQuality">
190 <param name="default_mapping_quality" type="integer" value="60" label="Default read mapping quality to assign to all reads"/>
191 </when>
192 <when value="Sample">
193 <param name="sample_to_keep" type="text" value="" label="The name of the sample(s) to keep, filtering out all others"/>
194 </when>
195 <when value="SingleReadGroup">
196 <param name="read_group_to_keep" type="integer" value="76" label="The name of the read group to keep, filtering out all others"/>
197 </when>
198 <when value="UnmappedRead">
199 <!-- no extra options -->
200 </when>
201 </conditional>
202 </repeat>
203 <repeat name="input_interval_repeat" title="Operate on Genomic intervals" help="-L,--intervals &amp;lt;intervals&amp;gt;">
204 <param name="input_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
205 </repeat>
206 <repeat name="input_exclude_interval_repeat" title="Exclude Genomic intervals" help="-XL,--excludeIntervals &amp;lt;excludeIntervals&amp;gt;">
207 <param name="input_exclude_intervals" type="data" format="bed,gatk_interval,picard_interval_list,vcf" label="Genomic intervals" />
208 </repeat>
209
210 <param name="interval_set_rule" type="select" label="Interval set rule" help="-isr,--interval_set_rule &amp;lt;interval_set_rule&amp;gt;">
211 <option value="UNION" selected="True">UNION</option>
212 <option value="INTERSECTION">INTERSECTION</option>
213 </param>
214
215 <conditional name="downsampling_type">
216 <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;">
217 <option value="NONE" selected="True">NONE</option>
218 <option value="ALL_READS">ALL_READS</option>
219 <option value="BY_SAMPLE">BY_SAMPLE</option>
220 </param>
221 <when value="NONE">
222 <!-- no more options here -->
223 </when>
224 <when value="ALL_READS">
225 <conditional name="downsample_to_type">
226 <param name="downsample_to_type_selector" type="select" label="Downsample method">
227 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
228 <option value="downsample_to_coverage">Downsample by Coverage</option>
229 </param>
230 <when value="downsample_to_fraction">
231 <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;"/>
232 </when>
233 <when value="downsample_to_coverage">
234 <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;"/>
235 </when>
236 </conditional>
237 </when>
238 <when value="BY_SAMPLE">
239 <conditional name="downsample_to_type">
240 <param name="downsample_to_type_selector" type="select" label="Downsample method">
241 <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
242 <option value="downsample_to_coverage">Downsample by Coverage</option>
243 </param>
244 <when value="downsample_to_fraction">
245 <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;"/>
246 </when>
247 <when value="downsample_to_coverage">
248 <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;"/>
249 </when>
250 </conditional>
251 </when>
252 </conditional>
253 <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine" help="-baq,--baq &amp;lt;baq&amp;gt;">
254 <option value="OFF" selected="True">OFF</option>
255 <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
256 <option value="RECALCULATE">RECALCULATE</option>
257 </param>
258 <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;" />
259 <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" help="-OQ,--useOriginalQualities" />
260 <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;"/>
261 <param name="validation_strictness" type="select" label="How strict should we be with validation" help="-S,--validation_strictness &amp;lt;validation_strictness&amp;gt;">
262 <option value="STRICT" selected="True">STRICT</option>
263 <option value="LENIENT">LENIENT</option>
264 <option value="SILENT">SILENT</option>
265 <!-- <option value="DEFAULT_STRINGENCY">DEFAULT_STRINGENCY</option> listed in docs, but not valid value...-->
266 </param>
267 <param name="interval_merging" type="select" label="Interval merging rule" help="-im,--interval_merging &amp;lt;interval_merging&amp;gt;">
268 <option value="ALL" selected="True">ALL</option>
269 <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
270 </param>
271
272 <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;">
273 <conditional name="read_group_black_list_type">
274 <param name="read_group_black_list_type_selector" type="select" label="Type of reads read group black list">
275 <option value="file" selected="True">Filters in file</option>
276 <option value="text">Specify filters as a string</option>
277 </param>
278 <when value="file">
279 <param name="read_group_black_list" type="data" format="txt" label="Read group black list file" />
280 </when>
281 <when value="text">
282 <param name="read_group_black_list" type="text" value="tag:string" label="Read group black list tag:string" />
283 </when>
284 </conditional>
285 </repeat>
286
287 <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"/>
288 <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"/>
289 <param name="fix_misencoded_quality_scores" type="boolean" truevalue="--fix_misencoded_quality_scores" falsevalue="" label="Fix mis-encoded base quality scores. Q0 == ASCII 33 according to the SAM specification, whereas Illumina encoding starts at Q64. The idea here is simple: we just iterate over all reads and subtract 31 from every quality score." checked="False" help="-fixMisencodedQuals / --fix_misencoded_quality_scores"/>
290
291 </when>
292 </conditional>
293 </xml>
294 <xml name="analysis_type_conditional">
295 <conditional name="analysis_param_type">
296 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
297 <option value="basic" selected="True">Basic</option>
298 <option value="advanced">Advanced</option>
299 </param>
300 <when value="basic">
301 <!-- Do nothing here -->
302 </when>
303 <when value="advanced">
304 <yield />
305 </when>
306 </conditional>
307 </xml>
308 <xml name="reference_source_selector_param">
309 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
310 <option value="cached">Locally cached</option>
311 <option value="history">History</option>
312 </param>
313 </xml>
314 <token name="@CITATION_SECTION@">------
315
316 **Citation**
317
318 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;`_
319
320 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
321
322 </token>
323 </macros>