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comparison macros.xml @ 0:504de035ac0f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/artbio_mutect2 commit b42fd0507a42663722f06ff0cedfee83a64c84b2"
author artbio
date Thu, 07 May 2020 12:29:36 -0400
parents
children 2b6ee93fd144
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-1:000000000000 0:504de035ac0f
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@VERSION@">4.1.4.0</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 <!--BAM input-->
293 <template name="picard_tumor_bam_input">
294 --INPUT tumor.bam
295 </template>
296
297 <template name="gatk_tumor_bam_input">
298 --input tumor.bam
299 </template>
300
301 <template name="tumor_bam_index_pre_chth"><![CDATA[
302 #for $sect in $sections
303 #if $varExists($sect + "tumor")
304 #if $getVar($sect + "tumor").is_of_type("bam")
305 ln -s $getVar($sect + "tumor") tumor.bam &&
306 samtools index tumor.bam &&
307 #else
308 ln -s $getVar($sect + "tumor") tumor.sam &&
309 samtools view -bS tumor.sam -o tumor.bam &&
310 samtools index tumor.bam &&
311 #end if
312 #end if
313 #end for
314 ]]></template>
315
316 <xml name="gatk_tumor_bam_req_params">
317 <param name="tumor" argument="--tumor" type="data" format="bam,sam" label="Input Tumor BAM/SAM/CRAM file" />
318 </xml>
319
320 <template name="picard_tumor_bam_index"><![CDATA[
321 #if $tumor.is_of_type("bam")
322 ln -s $INPUT tumor.bam &&
323 samtools index tumor.bam &&
324 #else
325 ln -s $INPUT tumor.sam &&
326 samtools view -bS tumor.sam -o tumor.bam &&
327 samtools index tumor.bam &&
328 #end if
329 ]]></template>
330
331 <template name="picard_normal_bam_input">
332 --INPUT normal.bam
333 </template>
334
335 <template name="gatk_normal_bam_input">
336 --input normal.bam
337 </template>
338
339 <template name="normal_bam_index_pre_chth"><![CDATA[
340 #for $sect in $sections
341 #if $varExists($sect + "normal")
342 #if $getVar($sect + "normal").is_of_type("bam")
343 ln -s $getVar($sect + "normal") normal.bam &&
344 samtools index normal.bam &&
345 #else
346 ln -s $getVar($sect + "normal") normal.sam &&
347 samtools view -bS normal.sam -o normal.bam &&
348 samtools index normal.bam &&
349 #end if
350 #end if
351 #end for
352 ]]></template>
353
354 <xml name="gatk_normal_bam_req_params">
355 <param name="normal" argument="--normal" type="data" format="bam,sam" label="Input Tumor BAM/SAM/CRAM file" />
356 </xml>
357
358 <template name="picard_normal_bam_index"><![CDATA[
359 #if $normal.is_of_type("bam")
360 ln -s $INPUT normal.bam &&
361 samtools index normal.bam &&
362 #else
363 ln -s $INPUT normal.sam &&
364 samtools view -bS normal.sam -o normal.bam &&
365 samtools index normal.bam &&
366 #end if
367 ]]></template>
368
369 <!--Output goes to stdout, no output parameter exists.-->
370 <template name="stdout_to_output">
371 > output.txt
372 </template>
373
374 <xml name="stdout_to_output_params">
375 <data format="txt" name="output" label="${tool.name} on ${on_string}: txt" from_work_dir="output.txt" />
376 </xml>
377
378 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
379 <template name="gatk_input_multi"><![CDATA[
380 #for $num, $file in enumerate($variant)
381 #if $file.is_of_type("vcf_bgzip")
382 --variant input${num}.vcf.gz
383 #elif $file.is_of_type("txt")
384 --variant input${num}.list
385 #else
386 --variant input${num}.vcf
387 #end if
388 #end for
389 ]]></template>
390
391 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
392 <template name="gatk_input_single"><![CDATA[
393 #if $variant.is_of_type("vcf_bgzip")
394 --variant input${num}.vcf.gz
395 #elif $variant.is_of_type("txt")
396 --variant input${num}.list
397 #else
398 --variant input${num}.vcf
399 #end if
400 ]]></template>
401
402 <template name="gatk_tabix_multi"><![CDATA[
403 #for $num, $file in enumerate($variant)
404 #set datatype = $file.datatype
405 #if $file.is_of_type("vcf_bgzip")
406 ln -s $file input${num}.vcf.gz &&
407 tabix input${num}.vcf.gz &&
408 #elif $file.is_of_type("txt")
409 ln -s $file input${num}.list &&
410 #else
411 ln -s $file input${num}.vcf &&
412 #end if
413 #end for
414 ]]></template>
415
416 <xml name="vcf_input_params_multi">
417 <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)"/>
418 </xml>
419
420
421
422 <!--ABOVE HAS BEEN REVIEWED-->
423
424
425
426
427
428
429
430
431
432
433 <!--{-->
434 <!--"summary": "BAM/SAM/CRAM file containing reads",-->
435 <!--"name": "&#45;&#45;input",-->
436 <!--"synonyms": "-I",-->
437 <!--"type": "List[String]",-->
438 <!--"required": "yes",-->
439 <!--"fulltext": "",-->
440 <!--"defaultValue": "[]",-->
441 <!--"minValue": "NA",-->
442 <!--"maxValue": "NA",-->
443 <!--"minRecValue": "NA",-->
444 <!--"maxRecValue": "NA",-->
445 <!--"kind": "required",-->
446 <!--"options": []-->
447 <!--},-->
448 <!--Required BAM input, GATK tool, may be specified multiple times.-->
449 <!--BAM should be indexed on the fly.-->
450 <!--Parameter is required, so is not contained within a section.-->
451 <!--Only decriptor that makes this unique for all input parameters is the summary field.-->
452 <!--{'pre_chth': ['bam_index_pre_chth'],-->
453 <!--'main_chth': ['picard_bam_input'],-->
454 <!--'main_xml': ['gatk_bam_req_params']}},-->
455
456
457
458
459
460
461
462
463
464
465
466
467
468 <!--Macros for multiple input tools. List[File] in GATK json.-->
469 <template name="vcf_tabix_multi"><![CDATA[
470 #for $num, $file in enumerate($input)
471 #set datatype = $file.datatype
472 #if $file.is_of_type("vcf_bgzip")
473 ln -s $file input${num}.vcf.gz &&
474 tabix input${num}.vcf.gz &&
475 #else
476 ln -s $file input${num}.vcf &&
477 #end if
478 #end for
479 ]]></template>
480
481 <template name="vcf_input_multi_picard"><![CDATA[
482 #for $num, $file in enumerate($input)
483 #if $file.is_of_type("vcf_bgzip")
484 --INPUT input${num}.vcf.gz
485 #else
486 --INPUT input${num}.vcf
487 #end if
488 #end for
489 ]]></template>
490
491 <template name="vcf_input_multi"><![CDATA[
492 #for $num, $file in enumerate($input)
493 #if $file.is_of_type("vcf_bgzip")
494 --input input${num}.vcf.gz
495 #else
496 --input input${num}.vcf
497 #end if
498 #end for
499 ]]></template>
500
501
502 <!--Picard single input tools-->
503 <template name="vcf_tabix"><![CDATA[
504 #set datatype = $input.datatype
505 #if $input.is_of_type("vcf_bgzip")
506 ln -s $input input.vcf.gz &&
507 tabix input.vcf.gz &&
508 #else
509 ln -s $input input.vcf &&
510 #end if
511 ]]></template>
512
513 <template name="gatk_tabix"><![CDATA[
514 #set datatype = $variant.datatype
515 #if $variant.is_of_type("vcf_bgzip")
516 ln -s $variant input.vcf.gz &&
517 tabix input.vcf.gz &&
518 #else
519 ln -s $variant input.vcf &&
520 gatk IndexFeatureFile -F input.vcf &&
521 #end if
522 ]]></template>
523
524 <template name="vcf_input_picard"><![CDATA[
525 #if $input.is_of_type("vcf_bgzip")
526 --INPUT input.vcf.gz
527 #else
528 --INPUT input.vcf
529 #end if
530 ]]></template>
531
532 <template name="vcf_input"><![CDATA[
533 #if $input.is_of_type("vcf_bgzip")
534 --input input.vcf.gz
535 #else
536 --input input.vcf
537 #end if
538 ]]></template>
539
540 <template name="gatk_input"><![CDATA[
541 #if $variant.is_of_type("vcf_bgzip")
542 --variant input.vcf.gz
543 #else
544 --variant input.vcf
545 #end if
546 ]]></template>
547
548 <template name="gatk_gvcf_tabix"><![CDATA[
549 #if $variant
550 ln -s $variant input.g.vcf &&
551 #end if
552 ]]></template>
553
554 <template name="gatk_gvcf_input"><![CDATA[
555 --variant input.g.vcf
556 ]]></template>
557
558 <xml name="gatk_gvcf_input_params">
559 <param name="variant" type="data" multiple="false" format="vcf" label="Input gVCF file" help=""/>
560 </xml>
561
562 <xml name="vcf_input_params">
563 <param name="input" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
564 </xml>
565
566 <xml name="gatk_vcf_input_params">
567 <param name="variant" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="A VCF file containing variants."/>
568 </xml>
569
570 <xml name="gatk_vcf_input_params_multi">
571 <param name="variant" type="data" multiple="true" format="vcf,vcf_bgzip,txt" label="Input VCF file(s)" help="A VCF file containing variants or a list of VCFs. Can be specified multiple times."/>
572 </xml>
573
574 <xml name="gatk_req_params">
575 <param name="input" type="data" format="bam,sam,cram" label="Input BAM/SAM/CRAM file" />
576 </xml>
577
578 <!--HDF5 Inputs-->
579
580 <xml name="hdf5_input">
581 <param name="input" type="data" format="h5,tabular" label="Input TSV or HDF5" help="Input TSV or HDF5 file containing integer read counts in genomic intervals for a single case sample (output of CollectReadCounts)." />
582 </xml>
583
584 <template name="hdf5_input_chth"><![CDATA[
585 --input "${input}"
586 ]]></template>
587
588 <template name="hdf5_output_chth">
589 --output "${output}"
590 </template>
591
592 <xml name="hdf5_output">
593 <data format="h5" name="output" label="${tool.name} on ${on_string}: HDF5" help="Output file for read counts." />
594 </xml>
595
596 <!--Output specific to ModelSegments. Files created based on prefix, so force that to be what we want, then pull important files with from_work_dir.-->
597 <!--${SAMPLE}.cr.seg-->
598 <!--${SAMPLE}.modelFinal.seg-->
599 <template name="modelsegments_chth"><![CDATA[
600 --output "."
601 --output-prefix "modelsegments"
602 ]]></template>
603
604 <xml name="modelsegments_output">
605 <data format="tabular" name="cr_seg" label="${tool.name} on ${on_string}: cr.seg" help="Copy-ratio segments." from_work_dir="modelsegments.cr.seg"/>
606 <data format="tabular" name="modelfinal_seg" label="${tool.name} on ${on_string}: modelFinal.seg" help="Modeled Segments" from_work_dir="modelsegments.modelFinal.seg"/>
607 </xml>
608
609 <!--deltaMAD.txt-->
610 <!--denoisedLimit4.png-->
611 <!--denoisedMAD.txt-->
612 <!--denoised.png-->
613 <!--scaledDeltaMAD.txt-->
614 <!--modeled.png-->
615 <!--standardizedMAD.txt-->
616
617 <template name="plotmodeledsegments_chth"><![CDATA[
618 --output "."
619 --output-prefix "plotmodeledsegments"
620 ]]></template>
621
622 <xml name="plotmodeledsegments_output">
623 <data format="png" name="modeled_png" label="${tool.name} on ${on_string}: modeled.png" help="Copy-Ratio Plot" from_work_dir="plotmodeledsegments.modeled.png"/>
624 </xml>
625
626 <!--Common Picard options-->
627 <template name="picard_opts">
628 #if $picard_adv.arguments_file
629 --arguments_file ${picard_adv.arguments_file}
630 #end if
631 --COMPRESSION_LEVEL ${picard_adv.COMPRESSION_LEVEL}
632 #if $picard_adv.GA4GH_CLIENT_SECRETS
633 --GA4GH_CLIENT_SECRETS ${picard_adv.GA4GH_CLIENT_SECRETS}
634 #end if
635 --MAX_RECORDS_IN_RAM ${picard_adv.MAX_RECORDS_IN_RAM}
636 --VALIDATION_STRINGENCY ${picard_adv.VALIDATION_STRINGENCY}
637 --VERBOSITY ${picard_adv.VERBOSITY}
638 ${picard_adv.CREATE_MD5_FILE}
639 ${picard_adv.USE_JDK_DEFLATER}
640 ${picard_adv.USE_JDK_INFLATER}
641 </template>
642
643 <xml name="picard_params">
644 <section name="picard_adv" title="Advanced Picard Options (Only change these if you know what you're doing.)" expanded="False">
645 <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" />
646 <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)." />
647 <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." />
648 <param argument="--GA4GH_CLIENT_SECRETS" type="data" format="json" optional="true" label="Ga4Gh Client Secrets" help="Google Genomics API client_secrets.json file path." />
649 <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." />
650 <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." />
651 <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" />
652 <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" />
653 <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." >
654 <option value="STRICT" selected="true">STRICT</option>
655 <option value="LENIENT" selected="false">LENIENT</option>
656 <option value="SILENT" selected="false">SILENT</option>
657 </param>
658 <param argument="--VERBOSITY" type="select" optional="true" label="Verbosity" help="Control verbosity of logging." >
659 <option value="ERROR" selected="false">ERROR</option>
660 <option value="WARNING" selected="false">WARNING</option>
661 <option value="INFO" selected="true">INFO</option>
662 <option value="DEBUG" selected="false">DEBUG</option>
663 </param>
664 </section>
665 </xml>
666
667 <!--Provides option to create gzipped output for VCF files-->
668 <xml name="gzip_vcf_params">
669 <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." />
670 </xml>
671
672 <!--Output related Picard options-->
673 <xml name="gzip_vcf_output_params">
674 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" >
675 <filter>not gzipped_output</filter>
676 </data>
677 <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >
678 <filter>gzipped_output</filter>
679 </data>
680 </xml>
681
682
683 <!--These are the same, other than the capitalization of output, so maybe a better way to do this.-->
684 <template name="picard_vcf_output_opts">
685 #if $gzipped_output
686 --OUTPUT output.vcf.gz
687 #else
688 --OUTPUT output.vcf
689 #end if
690 </template>
691
692 <template name="vcf_output_opts">
693 #if $gzipped_output
694 --output output.vcf.gz
695 #else
696 --output output.vcf
697 #end if
698 </template>
699
700 <xml name="picard_output_params">
701 <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >
702 <filter>picard_adv['CREATE_MD5_FILE']</filter>
703 </data>
704 </xml>
705
706
707 <!--<template name="ref_opts">-->
708 <!--#set $sections = ['optional','advanced','deprecated','']-->
709 <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")-->
710 <!--#for $sect in $sections-->
711 <!--#if $varExists('$sect.reference_source.reference_source_selector')-->
712 <!--#if $sect.reference_source.reference_source_selector != "no_ref"-->
713 <!--#if $sect.reference_source.reference_source_selector != "history"-->
714 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence.fields.path}-->
715 <!--#else-->
716 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence}-->
717 <!--#end if-->
718 <!--#end if-->
719 <!--#end if-->
720 <!--#end for-->
721 <!--</template>-->
722
723
724 <!--<template name="ref_opts_opt">-->
725 <!--#if $optional.reference_source.reference_source_selector != "no_ref"-->
726 <!--#if $optional.reference_source.reference_source_selector != "history"-->
727 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence.fields.path}-->
728 <!--#else-->
729 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence}-->
730 <!--#end if-->
731 <!--#end if-->
732 <!--</template>-->
733
734
735 <!--Citations-->
736 <xml name="citations">
737 <citation type="doi">10.1101/gr.107524.110</citation>
738 <citation type="doi">10.1038/ng.806</citation>
739 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
740 <citation type="doi">10.1101/201178</citation>
741 <yield />
742 </xml>
743
744 </macros>