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comparison macros.xml @ 0:f41a1e03538b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522"
author iuc
date Wed, 30 Oct 2019 15:33:59 -0400
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children fd2d6e035c3f
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-1:000000000000 0:f41a1e03538b
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@VERSION@">4.1.4.0</token>
4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy</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 <!--Command token, java options should not be hard coded here.-->
21 <token name="@CMD_BEGIN@">[[ -z \$_JAVA_OPTIONS ]] &amp;&amp; export JAVA_OPTS=\$_JAVA_OPTIONS &amp;&amp; gatk</token>
22
23 <!--Define sections that parameters could exist within.-->
24 <template name="set_sections">
25 #set global $sections = ['', 'optional.', 'advanced.', 'common.', 'deprecated.']
26 </template>
27
28 <!--Reference genome handling-->
29 <!--One template each for the different reference genome parameter names.-->
30 <!--TODO: Can the reference parameters all be the same?-->
31 <xml name="ref_sel">
32 <conditional name="reference_source">
33 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
34 <option value="cached">Locally cached</option>
35 <option value="history">History</option>
36 <option value="no_ref" selected="true">Do not pass</option>
37 </param>
38 <when value="cached">
39 <param name="reference_sequence" type="select" label="Reference" help="Reference sequence file." >
40 <options from_data_table="all_fasta" >
41 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
42 </options>
43 </param>
44 </when>
45 <when value="history">
46 <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Reference sequence file." />
47 </when>
48 <when value="no_ref" />
49 </conditional>
50 </xml>
51
52 <template name="ref_opts">
53 #for $sect in $sections
54 #if $varExists($sect + "reference_source.reference_source_selector")
55 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
56 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
57 --reference $getVar($sect + "reference_source.reference_sequence.fields.path")
58 #else
59 --reference reference.fa
60 #end if
61 #end if
62 #end if
63 #end for
64 </template>
65
66 <template name="picard_ref_opts">
67 #for $sect in $sections
68 #if $varExists($sect + "reference_source.reference_source_selector")
69 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
70 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
71 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
72 #else
73 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence")
74 #end if
75 #end if
76 #end if
77 #end for
78 </template>
79
80 <template name="picard_ref_opts_plain">
81 #for $sect in $sections
82 #if $varExists($sect + "reference_source.reference_source_selector")
83 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
84 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
85 --REFERENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
86 #else
87 --REFERENCE $getVar($sect + "reference_source.reference_sequence")
88 #end if
89 #end if
90 #end if
91 #end for
92 </template>
93
94 <template name="ref_opts_input">
95 #for $sect in $sections
96 #if $varExists($sect + "reference_source.reference_source_selector")
97 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
98 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
99 --input $getVar($sect + "reference_source.reference_sequence.fields.path")
100 #else
101 --input $getVar($sect + "reference_source.reference_sequence")
102 #end if
103 #end if
104 #end if
105 #end for
106 </template>
107
108
109 <!--Interval Macros-->
110 <template name="gatk_ints_chth">
111 #for $sect in $sections
112 #if $varExists($sect + "ival_type.ival_type_sel")
113 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
114 #if $varExists($sect + "ival_type.intervals")
115 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
116 --intervals intervals.interval_list
117 #end if
118 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
119 --intervals intervals.bed
120 #end if
121 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
122 --intervals intervals.vcf
123 #end if
124 #end if
125 #else
126 #if $varExists($sect + "ival_type.intervals")
127 --intervals $getVar($sect + "ival_type.intervals")
128 #end if
129 #end if
130 #if $varExists($sect + "ival_type.interval_padding")
131 --interval-padding $getVar($sect + "ival_type.interval_padding")
132 #end if
133 #end if
134 #end for
135 </template>
136
137
138 <template name="pre_gatk_ints_chth"><![CDATA[
139 #for $sect in $sections
140 #if $varExists($sect + "ival_type.ival_type_sel")
141 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
142 #if $varExists($sect + "ival_type.intervals")
143 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
144 ln -s $getVar($sect + "ival_type.intervals") intervals.interval_list &&
145 #end if
146 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
147 ln -s $getVar($sect + "ival_type.intervals") intervals.bed &&
148 #end if
149 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
150 ln -s $getVar($sect + "ival_type.intervals") intervals.vcf &&
151 #end if
152 #end if
153 #end if
154 #end if
155 #end for
156 ]]></template>
157
158 <xml name="gatk_ints">
159 <conditional name="ival_type">
160 <param name="ival_type_sel" type="select" label="Choose Genomic Interval Source">
161 <option value="ival_file" selected="true">Interval File</option>
162 <option value="ival_text" selected="false">Interval Text Input</option>
163 </param>
164 <when value="ival_file">
165 <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"/>
166 <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."/>
167 </when>
168 <when value="ival_text">
169 <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."/>
170 <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."/>
171 </when>
172 </conditional>
173 </xml>
174
175
176 <!--Exclude Intervals-->
177 <xml name="gatk_excl_ints">
178 <conditional name="excl_ival_type">
179 <param name="excl_ival_type_sel" type="select" label="Choose Genomic Interval Exclusion Source">
180 <option value="excl_ival_file" selected="true">Exclude Interval File</option>
181 <option value="excl_ival_text" selected="false">Exclude Interval Text Input</option>
182 </param>
183 <when value="excl_ival_file">
184 <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"/>
185 <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."/>
186 </when>
187 <when value="excl_ival_text">
188 <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."/>
189 <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."/>
190 </when>
191 </conditional>
192 </xml>
193
194 <template name="gatk_excl_ints_chth">
195 #for $sect in $sections
196 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
197 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "ival_file"
198 #if $varExists($sect + "excl_ival_type.exclude_intervals")
199 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
200 --exclude-intervals excl_intervals.interval_list
201 #end if
202 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
203 --exclude-intervals excl_intervals.bed
204 #end if
205 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
206 --exclude-intervals excl_intervals.vcf
207 #end if
208 #end if
209 #elif $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_text"
210 #if $varExists($sect + "excl_ival_type.exclude_intervals")
211 --exclude-intervals $getVar($sect + "excl_ival_type.exclude_intervals")
212 #end if
213 #else
214 #pass
215 #end if
216 #if $varExists($sect + "excl_ival_type.interval_exclusion_padding")
217 --interval-exclusion-padding $getVar($sect + "excl_ival_type.interval_exclusion_padding")
218 #end if
219 #end if
220 #end for
221 </template>
222
223 <template name="pre_gatk_excl_ints_chth"><![CDATA[
224 #for $sect in $sections
225 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
226 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_file"
227 #if $varExists($sect + "excl_ival_type.exclude_intervals")
228 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
229 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.interval_list &&
230 #end if
231 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
232 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.bed &&
233 #end if
234 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
235 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.vcf &&
236 #end if
237 #end if
238 #end if
239 #end if
240 #end for
241 ]]></template>
242
243 <!--Sequence dictionary selection options for Picard type tools-->
244 <template name="picard_seqdict_opts">
245 #for $sect in $sections
246 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
247 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
248 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
249 #set seq_dict_loc = ''.join($getVar($sect + seqdict_source.seqdict_sequence).fields.path.split('.')[:-1]) + '.dict'
250 --SEQUENCE_DICTIONARY $seq_dict_loc
251 #else
252 --SEQUENCE_DICTIONARY $getVar($sect + "seqdict_source.seqdict_sequence")
253 #end if
254 #end if
255 #end if
256 #end for
257 </template>
258
259 <template name="gatk_seqdict">
260 #for $sect in $sections
261 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
262 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
263 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
264 #set $seq_dict_loc = ''.join($getVar($sect + "seqdict_source.seqdict_sequence").fields.path.split('.')[:-1]) + '.dict'
265 --sequence-dictionary $seq_dict_loc
266 #else
267 --sequence-dictionary $getVar($sect + "seqdict_source.seqdict_sequence")
268 #end if
269 #end if
270 #end if
271 #end for
272 </template>
273
274 <xml name="seq_dict_sel">
275 <conditional name="seqdict_source">
276 <param name="seqdict_source_selector" type="select" label="Choose the source for the sequence dictionary">
277 <option value="cached">Locally cached</option>
278 <option value="history">History</option>
279 <option value="no_seq_dict" selected="true">Do not pass</option>
280 </param>
281 <when value="cached">
282 <param name="seqdict_sequence" type="select" label="Sequence Dictionary" help="Sequence dictionary file." >
283 <options from_data_table="all_fasta" >
284 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
285 </options>
286 </param>
287 </when>
288 <when value="history">
289 <param name="seqdict_sequence" type="data" format="txt" label="Sequence Dictionary" help="Sequence dictionary file. Must be in dict format." />
290 </when>
291 <when value="no_seq_dict" />
292 </conditional>
293 </xml>
294
295 <!--BAM input-->
296 <template name="picard_bam_input">
297 --INPUT input.bam
298 </template>
299
300 <template name="gatk_bam_input">
301 --input input.bam
302 </template>
303
304 <template name="bam_index_pre_chth"><![CDATA[
305 #for $sect in $sections
306 #if $varExists($sect + "input")
307 #if $getVar($sect + "input").is_of_type("bam")
308 ln -s $getVar($sect + "input") input.bam &&
309 samtools index input.bam &&
310 #else
311 ln -s $getVar($sect + "input") input.sam &&
312 samtools view -bS input.sam -o input.bam &&
313 samtools index input.bam &&
314 #end if
315 #end if
316 #end for
317 ]]></template>
318
319 <xml name="gatk_bam_req_params">
320 <param argument="--input" type="data" format="bam,sam" label="Input BAM/SAM/CRAM file" />
321 </xml>
322
323 <template name="picard_bam_index"><![CDATA[
324 #if $input.is_of_type("bam")
325 ln -s $INPUT input.bam &&
326 samtools index input.bam &&
327 #else
328 ln -s $INPUT input.sam &&
329 samtools view -bS input.sam -o input.bam &&
330 samtools index input.bam &&
331 #end if
332 ]]></template>
333
334
335 <!--Output goes to stdout, no output parameter exists.-->
336 <template name="stdout_to_output">
337 > output.txt
338 </template>
339
340 <xml name="stdout_to_output_params">
341 <data format="txt" name="output" label="${tool.name} on ${on_string}: txt" from_work_dir="output.txt" />
342 </xml>
343
344 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
345 <template name="gatk_input_multi"><![CDATA[
346 #for $num, $file in enumerate($variant)
347 #if $file.is_of_type("vcf_bgzip")
348 --variant input${num}.vcf.gz
349 #elif $file.is_of_type("txt")
350 --variant input${num}.list
351 #else
352 --variant input${num}.vcf
353 #end if
354 #end for
355 ]]></template>
356
357 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
358 <template name="gatk_input_single"><![CDATA[
359 #if $variant.is_of_type("vcf_bgzip")
360 --variant input${num}.vcf.gz
361 #elif $variant.is_of_type("txt")
362 --variant input${num}.list
363 #else
364 --variant input${num}.vcf
365 #end if
366 ]]></template>
367
368 <template name="gatk_tabix_multi"><![CDATA[
369 #for $num, $file in enumerate($variant)
370 #set datatype = $file.datatype
371 #if $file.is_of_type("vcf_bgzip")
372 ln -s $file input${num}.vcf.gz &&
373 tabix input${num}.vcf.gz &&
374 #elif $file.is_of_type("txt")
375 ln -s $file input${num}.list &&
376 #else
377 ln -s $file input${num}.vcf &&
378 #end if
379 #end for
380 ]]></template>
381
382 <xml name="vcf_input_params_multi">
383 <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)"/>
384 </xml>
385
386
387
388 <!--ABOVE HAS BEEN REVIEWED-->
389
390
391
392
393
394
395
396
397
398
399 <!--{-->
400 <!--"summary": "BAM/SAM/CRAM file containing reads",-->
401 <!--"name": "&#45;&#45;input",-->
402 <!--"synonyms": "-I",-->
403 <!--"type": "List[String]",-->
404 <!--"required": "yes",-->
405 <!--"fulltext": "",-->
406 <!--"defaultValue": "[]",-->
407 <!--"minValue": "NA",-->
408 <!--"maxValue": "NA",-->
409 <!--"minRecValue": "NA",-->
410 <!--"maxRecValue": "NA",-->
411 <!--"kind": "required",-->
412 <!--"options": []-->
413 <!--},-->
414 <!--Required BAM input, GATK tool, may be specified multiple times.-->
415 <!--BAM should be indexed on the fly.-->
416 <!--Parameter is required, so is not contained within a section.-->
417 <!--Only decriptor that makes this unique for all input parameters is the summary field.-->
418 <!--{'pre_chth': ['bam_index_pre_chth'],-->
419 <!--'main_chth': ['picard_bam_input'],-->
420 <!--'main_xml': ['gatk_bam_req_params']}},-->
421
422
423
424
425
426
427
428
429
430
431
432
433
434 <!--Macros for multiple input tools. List[File] in GATK json.-->
435 <template name="vcf_tabix_multi"><![CDATA[
436 #for $num, $file in enumerate($input)
437 #set datatype = $file.datatype
438 #if $file.is_of_type("vcf_bgzip")
439 ln -s $file input${num}.vcf.gz &&
440 tabix input${num}.vcf.gz &&
441 #else
442 ln -s $file input${num}.vcf &&
443 #end if
444 #end for
445 ]]></template>
446
447 <template name="vcf_input_multi_picard"><![CDATA[
448 #for $num, $file in enumerate($input)
449 #if $file.is_of_type("vcf_bgzip")
450 --INPUT input${num}.vcf.gz
451 #else
452 --INPUT input${num}.vcf
453 #end if
454 #end for
455 ]]></template>
456
457 <template name="vcf_input_multi"><![CDATA[
458 #for $num, $file in enumerate($input)
459 #if $file.is_of_type("vcf_bgzip")
460 --input input${num}.vcf.gz
461 #else
462 --input input${num}.vcf
463 #end if
464 #end for
465 ]]></template>
466
467
468 <!--Picard single input tools-->
469 <template name="vcf_tabix"><![CDATA[
470 #set datatype = $input.datatype
471 #if $input.is_of_type("vcf_bgzip")
472 ln -s $input input.vcf.gz &&
473 tabix input.vcf.gz &&
474 #else
475 ln -s $input input.vcf &&
476 #end if
477 ]]></template>
478
479 <template name="gatk_tabix"><![CDATA[
480 #set datatype = $variant.datatype
481 #if $variant.is_of_type("vcf_bgzip")
482 ln -s $variant input.vcf.gz &&
483 tabix input.vcf.gz &&
484 #else
485 ln -s $variant input.vcf &&
486 gatk IndexFeatureFile -F input.vcf &&
487 #end if
488 ]]></template>
489
490 <template name="vcf_input_picard"><![CDATA[
491 #if $input.is_of_type("vcf_bgzip")
492 --INPUT input.vcf.gz
493 #else
494 --INPUT input.vcf
495 #end if
496 ]]></template>
497
498 <template name="vcf_input"><![CDATA[
499 #if $input.is_of_type("vcf_bgzip")
500 --input input.vcf.gz
501 #else
502 --input input.vcf
503 #end if
504 ]]></template>
505
506 <template name="gatk_input"><![CDATA[
507 #if $variant.is_of_type("vcf_bgzip")
508 --variant input.vcf.gz
509 #else
510 --variant input.vcf
511 #end if
512 ]]></template>
513
514 <template name="gatk_gvcf_tabix"><![CDATA[
515 #if $variant
516 ln -s $variant input.g.vcf &&
517 #end if
518 ]]></template>
519
520 <template name="gatk_gvcf_input"><![CDATA[
521 --variant input.g.vcf
522 ]]></template>
523
524 <xml name="gatk_gvcf_input_params">
525 <param name="variant" type="data" multiple="false" format="vcf" label="Input gVCF file" help=""/>
526 </xml>
527
528 <xml name="vcf_input_params">
529 <param name="input" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
530 </xml>
531
532 <xml name="gatk_vcf_input_params">
533 <param name="variant" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="A VCF file containing variants."/>
534 </xml>
535
536 <xml name="gatk_vcf_input_params_multi">
537 <param name="variant" type="data" multiple="true" format="vcf,vcf_bgzip,txt" label="Input VCF file(s)" help="A VCF file containing variants or a list of VCFs. Can be specified multiple times."/>
538 </xml>
539
540 <xml name="gatk_req_params">
541 <param name="input" type="data" format="bam,sam,cram" label="Input BAM/SAM/CRAM file" />
542 </xml>
543
544 <!--HDF5 Inputs-->
545
546 <xml name="hdf5_input">
547 <param name="input" type="data" format="h5,tabular" label="Input TSV or HDF5" help="Input TSV or HDF5 file containing integer read counts in genomic intervals for a single case sample (output of CollectReadCounts)." />
548 </xml>
549
550 <template name="hdf5_input_chth"><![CDATA[
551 --input "${input}"
552 ]]></template>
553
554 <template name="hdf5_output_chth">
555 --output "${output}"
556 </template>
557
558 <xml name="hdf5_output">
559 <data format="h5" name="output" label="${tool.name} on ${on_string}: HDF5" help="Output file for read counts." />
560 </xml>
561
562 <!--Output specific to ModelSegments. Files created based on prefix, so force that to be what we want, then pull important files with from_work_dir.-->
563 <!--${SAMPLE}.cr.seg-->
564 <!--${SAMPLE}.modelFinal.seg-->
565 <template name="modelsegments_chth"><![CDATA[
566 --output "."
567 --output-prefix "modelsegments"
568 ]]></template>
569
570 <xml name="modelsegments_output">
571 <data format="tabular" name="cr_seg" label="${tool.name} on ${on_string}: cr.seg" help="Copy-ratio segments." from_work_dir="modelsegments.cr.seg"/>
572 <data format="tabular" name="modelfinal_seg" label="${tool.name} on ${on_string}: modelFinal.seg" help="Modeled Segments" from_work_dir="modelsegments.modelFinal.seg"/>
573 </xml>
574
575 <!--deltaMAD.txt-->
576 <!--denoisedLimit4.png-->
577 <!--denoisedMAD.txt-->
578 <!--denoised.png-->
579 <!--scaledDeltaMAD.txt-->
580 <!--modeled.png-->
581 <!--standardizedMAD.txt-->
582
583 <template name="plotmodeledsegments_chth"><![CDATA[
584 --output "."
585 --output-prefix "plotmodeledsegments"
586 ]]></template>
587
588 <xml name="plotmodeledsegments_output">
589 <data format="png" name="modeled_png" label="${tool.name} on ${on_string}: modeled.png" help="Copy-Ratio Plot" from_work_dir="plotmodeledsegments.modeled.png"/>
590 </xml>
591
592 <!--Common Picard options-->
593 <template name="picard_opts">
594 #if $picard_adv.arguments_file
595 --arguments_file ${picard_adv.arguments_file}
596 #end if
597 --COMPRESSION_LEVEL ${picard_adv.COMPRESSION_LEVEL}
598 #if $picard_adv.GA4GH_CLIENT_SECRETS
599 --GA4GH_CLIENT_SECRETS ${picard_adv.GA4GH_CLIENT_SECRETS}
600 #end if
601 --MAX_RECORDS_IN_RAM ${picard_adv.MAX_RECORDS_IN_RAM}
602 --VALIDATION_STRINGENCY ${picard_adv.VALIDATION_STRINGENCY}
603 --VERBOSITY ${picard_adv.VERBOSITY}
604 ${picard_adv.CREATE_MD5_FILE}
605 ${picard_adv.USE_JDK_DEFLATER}
606 ${picard_adv.USE_JDK_INFLATER}
607 </template>
608
609 <xml name="picard_params">
610 <section name="picard_adv" title="Advanced Picard Options (Only change these if you know what you're doing.)" expanded="False">
611 <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" />
612 <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)." />
613 <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." />
614 <param argument="--GA4GH_CLIENT_SECRETS" type="data" format="json" optional="true" label="Ga4Gh Client Secrets" help="Google Genomics API client_secrets.json file path." />
615 <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." />
616 <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." />
617 <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" />
618 <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" />
619 <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." >
620 <option value="STRICT" selected="true">STRICT</option>
621 <option value="LENIENT" selected="false">LENIENT</option>
622 <option value="SILENT" selected="false">SILENT</option>
623 </param>
624 <param argument="--VERBOSITY" type="select" optional="true" label="Verbosity" help="Control verbosity of logging." >
625 <option value="ERROR" selected="false">ERROR</option>
626 <option value="WARNING" selected="false">WARNING</option>
627 <option value="INFO" selected="true">INFO</option>
628 <option value="DEBUG" selected="false">DEBUG</option>
629 </param>
630 </section>
631 </xml>
632
633 <!--Provides option to create gzipped output for VCF files-->
634 <xml name="gzip_vcf_params">
635 <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." />
636 </xml>
637
638 <!--Output related Picard options-->
639 <xml name="gzip_vcf_output_params">
640 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" >
641 <filter>not gzipped_output</filter>
642 </data>
643 <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >
644 <filter>gzipped_output</filter>
645 </data>
646 </xml>
647
648
649 <!--These are the same, other than the capitalization of output, so maybe a better way to do this.-->
650 <template name="picard_vcf_output_opts">
651 #if $gzipped_output
652 --OUTPUT output.vcf.gz
653 #else
654 --OUTPUT output.vcf
655 #end if
656 </template>
657
658 <template name="vcf_output_opts">
659 #if $gzipped_output
660 --output output.vcf.gz
661 #else
662 --output output.vcf
663 #end if
664 </template>
665
666 <xml name="picard_output_params">
667 <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >
668 <filter>picard_adv['CREATE_MD5_FILE']</filter>
669 </data>
670 </xml>
671
672
673 <!--<template name="ref_opts">-->
674 <!--#set $sections = ['optional','advanced','common','deprecated','']-->
675 <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")-->
676 <!--#for $sect in $sections-->
677 <!--#if $varExists('$sect.reference_source.reference_source_selector')-->
678 <!--#if $sect.reference_source.reference_source_selector != "no_ref"-->
679 <!--#if $sect.reference_source.reference_source_selector != "history"-->
680 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence.fields.path}-->
681 <!--#else-->
682 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence}-->
683 <!--#end if-->
684 <!--#end if-->
685 <!--#end if-->
686 <!--#end for-->
687 <!--</template>-->
688
689
690 <!--<template name="ref_opts_opt">-->
691 <!--#if $optional.reference_source.reference_source_selector != "no_ref"-->
692 <!--#if $optional.reference_source.reference_source_selector != "history"-->
693 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence.fields.path}-->
694 <!--#else-->
695 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence}-->
696 <!--#end if-->
697 <!--#end if-->
698 <!--</template>-->
699
700
701 <!--Citations-->
702 <xml name="citations">
703 <citation type="doi">10.1101/gr.107524.110</citation>
704 <citation type="doi">10.1038/ng.806</citation>
705 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
706 <citation type="doi">10.1101/201178</citation>
707 <yield />
708 </xml>
709
710 </macros>