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comparison macros.xml @ 0:c51c08cc9fcc draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
author artbio
date Wed, 29 Dec 2021 01:36:41 +0000
parents
children b040adcfeefd
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-1:000000000000 0:c51c08cc9fcc
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@VERSION@">4.1.7.0</token>
4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token>
5
6 <xml name="requirements">
7 <requirements>
8 <requirement type="package" version="@VERSION@">gatk4</requirement>
9 <requirement type="package" version="0.2.5">tabix</requirement>
10 <requirement type="package" version="1.9">samtools</requirement>
11 <yield />
12 </requirements>
13 </xml>
14
15 <!--Hacky way to determine GATK version, for display in tool info-->
16 <xml name="version_cmd">
17 <version_command>gatk SortSam --version 2>&amp;1 | grep Version | cut -d ':' -f 2</version_command>
18 </xml>
19
20 <!--Define sections that parameters could exist within.-->
21 <template name="set_sections">
22 #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.']
23 </template>
24
25 <!--Reference genome handling-->
26 <!--One template each for the different reference genome parameter names.-->
27 <!--TODO: Can the reference parameters all be the same?-->
28 <xml name="ref_sel">
29 <conditional name="reference_source">
30 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
31 <option value="cached">Locally cached</option>
32 <option value="history">History</option>
33 <option value="no_ref" selected="true">Do not pass</option>
34 </param>
35 <when value="cached">
36 <param name="reference_sequence" type="select" label="Reference" help="Reference sequence file." >
37 <options from_data_table="all_fasta" >
38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
39 </options>
40 </param>
41 </when>
42 <when value="history">
43 <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Reference sequence file." />
44 </when>
45 <when value="no_ref" />
46 </conditional>
47 </xml>
48
49 <template name="ref_opts">
50 #for $sect in $sections
51 #if $varExists($sect + "reference_source.reference_source_selector")
52 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
53 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
54 --reference $getVar($sect + "reference_source.reference_sequence.fields.path")
55 #else
56 --reference reference.fa
57 #end if
58 #end if
59 #end if
60 #end for
61 </template>
62
63 <template name="picard_ref_opts">
64 #for $sect in $sections
65 #if $varExists($sect + "reference_source.reference_source_selector")
66 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
67 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
68 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
69 #else
70 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence")
71 #end if
72 #end if
73 #end if
74 #end for
75 </template>
76
77 <template name="picard_ref_opts_plain">
78 #for $sect in $sections
79 #if $varExists($sect + "reference_source.reference_source_selector")
80 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
81 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
82 --REFERENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
83 #else
84 --REFERENCE $getVar($sect + "reference_source.reference_sequence")
85 #end if
86 #end if
87 #end if
88 #end for
89 </template>
90
91 <template name="ref_opts_input">
92 #for $sect in $sections
93 #if $varExists($sect + "reference_source.reference_source_selector")
94 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
95 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
96 --input $getVar($sect + "reference_source.reference_sequence.fields.path")
97 #else
98 --input $getVar($sect + "reference_source.reference_sequence")
99 #end if
100 #end if
101 #end if
102 #end for
103 </template>
104
105
106 <!--Interval Macros-->
107 <template name="gatk_ints_chth">
108 #for $sect in $sections
109 #if $varExists($sect + "ival_type.ival_type_sel")
110 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
111 #if $varExists($sect + "ival_type.intervals")
112 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
113 --intervals intervals.interval_list
114 #end if
115 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
116 --intervals intervals.bed
117 #end if
118 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
119 --intervals intervals.vcf
120 #end if
121 #end if
122 #else
123 #if $varExists($sect + "ival_type.intervals")
124 --intervals $getVar($sect + "ival_type.intervals")
125 #end if
126 #end if
127 #if $varExists($sect + "ival_type.interval_padding")
128 --interval-padding $getVar($sect + "ival_type.interval_padding")
129 #end if
130 #end if
131 #end for
132 </template>
133
134
135 <template name="pre_gatk_ints_chth"><![CDATA[
136 #for $sect in $sections
137 #if $varExists($sect + "ival_type.ival_type_sel")
138 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
139 #if $varExists($sect + "ival_type.intervals")
140 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
141 ln -s $getVar($sect + "ival_type.intervals") intervals.interval_list &&
142 #end if
143 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
144 ln -s $getVar($sect + "ival_type.intervals") intervals.bed &&
145 #end if
146 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
147 ln -s $getVar($sect + "ival_type.intervals") intervals.vcf &&
148 #end if
149 #end if
150 #end if
151 #end if
152 #end for
153 ]]></template>
154
155 <xml name="gatk_ints">
156 <conditional name="ival_type">
157 <param name="ival_type_sel" type="select" label="Choose Genomic Interval Source">
158 <option value="ival_file" selected="true">Interval File</option>
159 <option value="ival_text" selected="false">Interval Text Input</option>
160 </param>
161 <when value="ival_file">
162 <param name="intervals" argument="--intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Intervals File" help="One or more genomic intervals over which to operate"/>
163 <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
164 </when>
165 <when value="ival_text">
166 <param name="intervals" argument="--intervals" type="text" optional="true" label="Intervals Text Input" help="One or more genomic intervals over which to operate. Enter in chrom:start-stop format."/>
167 <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
168 </when>
169 </conditional>
170 </xml>
171
172
173 <!--Exclude Intervals-->
174 <xml name="gatk_excl_ints">
175 <conditional name="excl_ival_type">
176 <param name="excl_ival_type_sel" type="select" label="Choose Genomic Interval Exclusion Source">
177 <option value="excl_ival_file" selected="true">Exclude Interval File</option>
178 <option value="excl_ival_text" selected="false">Exclude Interval Text Input</option>
179 </param>
180 <when value="excl_ival_file">
181 <param name="exclude_intervals" argument="--exclude-intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Exclude Intervals File" help="One or more genomic intervals to exclude from processing"/>
182 <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
183 </when>
184 <when value="excl_ival_text">
185 <param name="exclude_intervals" argument="--exclude-intervals" type="text" optional="true" label="Exclude Intervals Text Input" help="One or more genomic intervals to exclude from processing. Enter in chrom:start-stop format."/>
186 <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
187 </when>
188 </conditional>
189 </xml>
190
191 <template name="gatk_excl_ints_chth">
192 #for $sect in $sections
193 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
194 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "ival_file"
195 #if $varExists($sect + "excl_ival_type.exclude_intervals")
196 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
197 --exclude-intervals excl_intervals.interval_list
198 #end if
199 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
200 --exclude-intervals excl_intervals.bed
201 #end if
202 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
203 --exclude-intervals excl_intervals.vcf
204 #end if
205 #end if
206 #elif $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_text"
207 #if $varExists($sect + "excl_ival_type.exclude_intervals")
208 --exclude-intervals $getVar($sect + "excl_ival_type.exclude_intervals")
209 #end if
210 #else
211 #pass
212 #end if
213 #if $varExists($sect + "excl_ival_type.interval_exclusion_padding")
214 --interval-exclusion-padding $getVar($sect + "excl_ival_type.interval_exclusion_padding")
215 #end if
216 #end if
217 #end for
218 </template>
219
220 <template name="pre_gatk_excl_ints_chth"><![CDATA[
221 #for $sect in $sections
222 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
223 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_file"
224 #if $varExists($sect + "excl_ival_type.exclude_intervals")
225 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
226 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.interval_list &&
227 #end if
228 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
229 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.bed &&
230 #end if
231 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
232 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.vcf &&
233 #end if
234 #end if
235 #end if
236 #end if
237 #end for
238 ]]></template>
239
240 <!--Sequence dictionary selection options for Picard type tools-->
241 <template name="picard_seqdict_opts">
242 #for $sect in $sections
243 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
244 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
245 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
246 #set seq_dict_loc = ''.join($getVar($sect + seqdict_source.seqdict_sequence).fields.path.split('.')[:-1]) + '.dict'
247 --SEQUENCE_DICTIONARY $seq_dict_loc
248 #else
249 --SEQUENCE_DICTIONARY $getVar($sect + "seqdict_source.seqdict_sequence")
250 #end if
251 #end if
252 #end if
253 #end for
254 </template>
255
256 <template name="gatk_seqdict">
257 #for $sect in $sections
258 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
259 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
260 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
261 #set $seq_dict_loc = ''.join($getVar($sect + "seqdict_source.seqdict_sequence").fields.path.split('.')[:-1]) + '.dict'
262 --sequence-dictionary $seq_dict_loc
263 #else
264 --sequence-dictionary $getVar($sect + "seqdict_source.seqdict_sequence")
265 #end if
266 #end if
267 #end if
268 #end for
269 </template>
270
271 <xml name="seq_dict_sel">
272 <conditional name="seqdict_source">
273 <param name="seqdict_source_selector" type="select" label="Choose the source for the sequence dictionary">
274 <option value="cached">Locally cached</option>
275 <option value="history">History</option>
276 <option value="no_seq_dict" selected="true">Do not pass</option>
277 </param>
278 <when value="cached">
279 <param name="seqdict_sequence" type="select" label="Sequence Dictionary" help="Sequence dictionary file." >
280 <options from_data_table="all_fasta" >
281 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
282 </options>
283 </param>
284 </when>
285 <when value="history">
286 <param name="seqdict_sequence" type="data" format="txt" label="Sequence Dictionary" help="Sequence dictionary file. Must be in dict format." />
287 </when>
288 <when value="no_seq_dict" />
289 </conditional>
290 </xml>
291
292 <!--Output goes to stdout, no output parameter exists.-->
293 <template name="stdout_to_output">
294 > output.txt
295 </template>
296
297 <xml name="stdout_to_output_params">
298 <data format="txt" name="output" label="${tool.name} on ${on_string}: txt" from_work_dir="output.txt" />
299 </xml>
300
301 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
302 <template name="gatk_input_multi"><![CDATA[
303 #for $num, $file in enumerate($variant)
304 #if $file.is_of_type("vcf_bgzip")
305 --variant input${num}.vcf.gz
306 #elif $file.is_of_type("txt")
307 --variant input${num}.list
308 #else
309 --variant input${num}.vcf
310 #end if
311 #end for
312 ]]></template>
313
314 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
315 <template name="gatk_input_single"><![CDATA[
316 #if $variant.is_of_type("vcf_bgzip")
317 --variant input${num}.vcf.gz
318 #elif $variant.is_of_type("txt")
319 --variant input${num}.list
320 #else
321 --variant input${num}.vcf
322 #end if
323 ]]></template>
324
325 <template name="gatk_tabix_multi"><![CDATA[
326 #for $num, $file in enumerate($variant)
327 #set datatype = $file.datatype
328 #if $file.is_of_type("vcf_bgzip")
329 ln -s $file input${num}.vcf.gz &&
330 tabix input${num}.vcf.gz &&
331 #elif $file.is_of_type("txt")
332 ln -s $file input${num}.list &&
333 #else
334 ln -s $file input${num}.vcf &&
335 #end if
336 #end for
337 ]]></template>
338
339 <xml name="vcf_input_params_multi">
340 <param name="input" type="data" multiple="true" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
341 </xml>
342
343
344
345 <!--ABOVE HAS BEEN REVIEWED-->
346
347
348
349
350
351
352
353
354
355
356 <!--{-->
357 <!--"summary": "BAM/SAM/CRAM file containing reads",-->
358 <!--"name": "&#45;&#45;input",-->
359 <!--"synonyms": "-I",-->
360 <!--"type": "List[String]",-->
361 <!--"required": "yes",-->
362 <!--"fulltext": "",-->
363 <!--"defaultValue": "[]",-->
364 <!--"minValue": "NA",-->
365 <!--"maxValue": "NA",-->
366 <!--"minRecValue": "NA",-->
367 <!--"maxRecValue": "NA",-->
368 <!--"kind": "required",-->
369 <!--"options": []-->
370 <!--},-->
371 <!--Required BAM input, GATK tool, may be specified multiple times.-->
372 <!--BAM should be indexed on the fly.-->
373 <!--Parameter is required, so is not contained within a section.-->
374 <!--Only decriptor that makes this unique for all input parameters is the summary field.-->
375 <!--{'pre_chth': ['bam_index_pre_chth'],-->
376 <!--'main_chth': ['picard_bam_input'],-->
377 <!--'main_xml': ['gatk_bam_req_params']}},-->
378
379
380
381
382
383
384
385
386
387
388
389
390
391 <!--Macros for multiple input tools. List[File] in GATK json.-->
392 <template name="vcf_tabix_multi"><![CDATA[
393 #for $num, $file in enumerate($input)
394 #set datatype = $file.datatype
395 #if $file.is_of_type("vcf_bgzip")
396 ln -s $file input${num}.vcf.gz &&
397 tabix input${num}.vcf.gz &&
398 #else
399 ln -s $file input${num}.vcf &&
400 #end if
401 #end for
402 ]]></template>
403
404 <template name="vcf_input_multi_picard"><![CDATA[
405 #for $num, $file in enumerate($input)
406 #if $file.is_of_type("vcf_bgzip")
407 --INPUT input${num}.vcf.gz
408 #else
409 --INPUT input${num}.vcf
410 #end if
411 #end for
412 ]]></template>
413
414 <template name="vcf_input_multi"><![CDATA[
415 #for $num, $file in enumerate($input)
416 #if $file.is_of_type("vcf_bgzip")
417 --input input${num}.vcf.gz
418 #else
419 --input input${num}.vcf
420 #end if
421 #end for
422 ]]></template>
423
424
425 <!--Picard single input tools-->
426 <template name="vcf_tabix"><![CDATA[
427 #set datatype = $input.datatype
428 #if $input.is_of_type("vcf_bgzip")
429 ln -s $input input.vcf.gz &&
430 tabix input.vcf.gz &&
431 #else
432 ln -s $input input.vcf &&
433 #end if
434 ]]></template>
435
436 <template name="gatk_tabix"><![CDATA[
437 #set datatype = $variant.datatype
438 #if $variant.is_of_type("vcf_bgzip")
439 ln -s $variant input.vcf.gz &&
440 tabix input.vcf.gz &&
441 #else
442 ln -s $variant input.vcf &&
443 gatk IndexFeatureFile -F input.vcf &&
444 #end if
445 ]]></template>
446
447 <template name="vcf_input_picard"><![CDATA[
448 #if $input.is_of_type("vcf_bgzip")
449 --INPUT input.vcf.gz
450 #else
451 --INPUT input.vcf
452 #end if
453 ]]></template>
454
455 <template name="vcf_input"><![CDATA[
456 #if $input.is_of_type("vcf_bgzip")
457 --input input.vcf.gz
458 #else
459 --input input.vcf
460 #end if
461 ]]></template>
462
463 <template name="gatk_input"><![CDATA[
464 #if $variant.is_of_type("vcf_bgzip")
465 --variant input.vcf.gz
466 #else
467 --variant input.vcf
468 #end if
469 ]]></template>
470
471 <template name="gatk_gvcf_tabix"><![CDATA[
472 #if $variant
473 ln -s $variant input.g.vcf &&
474 #end if
475 ]]></template>
476
477 <template name="gatk_gvcf_input"><![CDATA[
478 --variant input.g.vcf
479 ]]></template>
480
481 <xml name="gatk_gvcf_input_params">
482 <param name="variant" type="data" multiple="false" format="vcf" label="Input gVCF file" help=""/>
483 </xml>
484
485 <xml name="vcf_input_params">
486 <param name="input" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
487 </xml>
488
489 <xml name="gatk_vcf_input_params">
490 <param name="variant" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="A VCF file containing variants."/>
491 </xml>
492
493 <xml name="gatk_vcf_input_params_multi">
494 <param name="variant" type="data" multiple="true" format="vcf,vcf_bgzip,txt" label="Input VCF file(s)" help="A VCF file containing variants or a list of VCFs. Can be specified multiple times."/>
495 </xml>
496
497 <xml name="gatk_req_params">
498 <param name="input" type="data" format="bam,sam,cram" label="Input BAM/SAM/CRAM file" />
499 </xml>
500
501 <!--HDF5 Inputs-->
502
503 <xml name="hdf5_input">
504 <param name="input" type="data" format="h5,tabular" label="Input TSV or HDF5" help="Input TSV or HDF5 file containing integer read counts in genomic intervals for a single case sample (output of CollectReadCounts)." />
505 </xml>
506
507 <template name="hdf5_input_chth"><![CDATA[
508 --input "${input}"
509 ]]></template>
510
511 <template name="hdf5_output_chth">
512 --output "${output}"
513 </template>
514
515 <xml name="hdf5_output">
516 <data format="h5" name="output" label="${tool.name} on ${on_string}: HDF5" help="Output file for read counts." />
517 </xml>
518
519 <!--Output specific to ModelSegments. Files created based on prefix, so force that to be what we want, then pull important files with from_work_dir.-->
520 <!--${SAMPLE}.cr.seg-->
521 <!--${SAMPLE}.modelFinal.seg-->
522 <template name="modelsegments_chth"><![CDATA[
523 --output "."
524 --output-prefix "modelsegments"
525 ]]></template>
526
527 <xml name="modelsegments_output">
528 <data format="tabular" name="cr_seg" label="${tool.name} on ${on_string}: cr.seg" help="Copy-ratio segments." from_work_dir="modelsegments.cr.seg"/>
529 <data format="tabular" name="modelfinal_seg" label="${tool.name} on ${on_string}: modelFinal.seg" help="Modeled Segments" from_work_dir="modelsegments.modelFinal.seg"/>
530 </xml>
531
532 <!--deltaMAD.txt-->
533 <!--denoisedLimit4.png-->
534 <!--denoisedMAD.txt-->
535 <!--denoised.png-->
536 <!--scaledDeltaMAD.txt-->
537 <!--modeled.png-->
538 <!--standardizedMAD.txt-->
539
540 <template name="plotmodeledsegments_chth"><![CDATA[
541 --output "."
542 --output-prefix "plotmodeledsegments"
543 ]]></template>
544
545 <xml name="plotmodeledsegments_output">
546 <data format="png" name="modeled_png" label="${tool.name} on ${on_string}: modeled.png" help="Copy-Ratio Plot" from_work_dir="plotmodeledsegments.modeled.png"/>
547 </xml>
548
549 <!--Common Picard options-->
550 <template name="picard_opts">
551 #if $picard_adv.arguments_file
552 --arguments_file ${picard_adv.arguments_file}
553 #end if
554 --COMPRESSION_LEVEL ${picard_adv.COMPRESSION_LEVEL}
555 #if $picard_adv.GA4GH_CLIENT_SECRETS
556 --GA4GH_CLIENT_SECRETS ${picard_adv.GA4GH_CLIENT_SECRETS}
557 #end if
558 --MAX_RECORDS_IN_RAM ${picard_adv.MAX_RECORDS_IN_RAM}
559 --VALIDATION_STRINGENCY ${picard_adv.VALIDATION_STRINGENCY}
560 --VERBOSITY ${picard_adv.VERBOSITY}
561 ${picard_adv.CREATE_MD5_FILE}
562 ${picard_adv.USE_JDK_DEFLATER}
563 ${picard_adv.USE_JDK_INFLATER}
564 </template>
565
566 <xml name="picard_params">
567 <section name="picard_adv" title="Advanced Picard Options (Only change these if you know what you're doing.)" expanded="False">
568 <param argument="--arguments_file" type="data" optional="true" format="txt" label="Arguments File" help="read one or more arguments files and add them to the command line" />
569 <param argument="--COMPRESSION_LEVEL" type="integer" optional="true" value="5" min="1" max="9" label="Compression Level" help="Compression level for all compressed files created (e.g. BAM and VCF)." />
570 <param argument="--CREATE_MD5_FILE" truevalue="--CREATE_MD5_FILE" falsevalue="" type="boolean" optional="true" checked="false" label="Create MD5 File" help="Whether to create an MD5 digest for any BAM or FASTQ files created." />
571 <param argument="--GA4GH_CLIENT_SECRETS" type="data" format="json" optional="true" label="Ga4Gh Client Secrets" help="Google Genomics API client_secrets.json file path." />
572 <param argument="--MAX_RECORDS_IN_RAM" type="integer" optional="true" value="500000" label="Max Records In Ram" help="When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed." />
573 <param argument="--TMP_DIR" type="text" optional="true" label="Tmp Dir" help="One or more directories with space available to be used by this program for temporary storage of working files. Keep in mind, you must be able to access this directory from either your user, or from the Galaxy user, depending on your configuration." />
574 <param argument="--USE_JDK_DEFLATER" truevalue="--USE_JDK_DEFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Deflater" help="Use the JDK Deflater instead of the Intel Deflater for writing compressed output" />
575 <param argument="--USE_JDK_INFLATER" truevalue="--USE_JDK_INFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Inflater" help="Use the JDK Inflater instead of the Intel Inflater for reading compressed input" />
576 <param argument="--VALIDATION_STRINGENCY" type="select" optional="true" label="Validation Stringency" help="Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded." >
577 <option value="STRICT" selected="true">STRICT</option>
578 <option value="LENIENT" selected="false">LENIENT</option>
579 <option value="SILENT" selected="false">SILENT</option>
580 </param>
581 <param argument="--VERBOSITY" type="select" optional="true" label="Verbosity" help="Control verbosity of logging." >
582 <option value="ERROR" selected="false">ERROR</option>
583 <option value="WARNING" selected="false">WARNING</option>
584 <option value="INFO" selected="true">INFO</option>
585 <option value="DEBUG" selected="false">DEBUG</option>
586 </param>
587 </section>
588 </xml>
589
590 <!--Provides option to create gzipped output for VCF files-->
591 <xml name="gzip_vcf_params">
592 <param name="gzipped_output" type="boolean" checked="true" label="GZIP Output?" help="If you would like gzipped output, check this box. In general, it would be preferable to do this, unless your downstream tool does not support handling of gzipped files." />
593 </xml>
594
595 <!--Output related Picard options-->
596 <xml name="gzip_vcf_output_params">
597 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" >
598 <filter>not gzipped_output</filter>
599 </data>
600 <data format="tabular" name="output_vcf_stats" label="gatk vcf stats" from_work_dir="output.vcf.stats" >
601 <filter>not gzipped_output</filter>
602 </data>
603 <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >
604 <filter>gzipped_output</filter>
605 </data>
606 <data format="tabular" name="output_vcf_bgzip_stats" label="gatk vcf stats" from_work_dir="output.vcf.gz.stats" >
607 <filter>gzipped_output</filter>
608 </data>
609 </xml>
610
611
612 <!--These are the same, other than the capitalization of output, so maybe a better way to do this.-->
613 <template name="picard_vcf_output_opts">
614 #if $gzipped_output
615 --OUTPUT output.vcf.gz
616 #else
617 --OUTPUT output.vcf
618 #end if
619 </template>
620
621 <template name="vcf_output_opts">
622 #if $gzipped_output
623 --output output.vcf.gz
624 #else
625 --output output.vcf
626 #end if
627 </template>
628
629 <xml name="picard_output_params">
630 <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >
631 <filter>picard_adv['CREATE_MD5_FILE']</filter>
632 </data>
633 </xml>
634
635
636 <!--<template name="ref_opts">-->
637 <!--#set $sections = ['optional','advanced','deprecated','']-->
638 <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")-->
639 <!--#for $sect in $sections-->
640 <!--#if $varExists('$sect.reference_source.reference_source_selector')-->
641 <!--#if $sect.reference_source.reference_source_selector != "no_ref"-->
642 <!--#if $sect.reference_source.reference_source_selector != "history"-->
643 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence.fields.path}-->
644 <!--#else-->
645 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence}-->
646 <!--#end if-->
647 <!--#end if-->
648 <!--#end if-->
649 <!--#end for-->
650 <!--</template>-->
651
652
653 <!--<template name="ref_opts_opt">-->
654 <!--#if $optional.reference_source.reference_source_selector != "no_ref"-->
655 <!--#if $optional.reference_source.reference_source_selector != "history"-->
656 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence.fields.path}-->
657 <!--#else-->
658 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence}-->
659 <!--#end if-->
660 <!--#end if-->
661 <!--</template>-->
662
663
664 <!--Citations-->
665 <xml name="citations">
666 <citation type="doi">10.1101/gr.107524.110</citation>
667 <citation type="doi">10.1038/ng.806</citation>
668 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
669 <citation type="doi">10.1101/201178</citation>
670 <yield />
671 </xml>
672
673 </macros>