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comparison deepvariant.xml @ 6:1ad55977a040 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
author iuc
date Thu, 12 Feb 2026 08:51:49 +0000
parents fd52f65372c9
children
comparison
equal deleted inserted replaced
5:fd52f65372c9 6:1ad55977a040
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='edam_ontology' /> 6 <expand macro='edam_ontology' />
7 <expand macro='requirements' /> 7 <expand macro='requirements' />
8 <command detect_errors='exit_code'><![CDATA[ 8 <command detect_errors='exit_code'><![CDATA[
9 ln -s '${reads}' reads_alignment.bam 9 ln -s '${reads}' 'reads_alignment.$reads.ext'
10 && ln -s '${reads.metadata.bam_index}' reads_alignment.bam.bai 10 #if $reads.is_of_type("bam")
11 && ln -s '${reads.metadata.bam_index}' reads_alignment.bam.bai
12 #elif $reads.is_of_type("cram")
13 && ln -s '${reads.metadata.cram_index}' reads_alignment.cram.crai
14 #end if
11 #if $regions_conditional.regions_option == 'bed' 15 #if $regions_conditional.regions_option == 'bed'
12 && ln -s '${regions_conditional.bed_file}' region.bed 16 && ln -s '${regions_conditional.bed_file}' region.bed
13 #end if 17 #end if
14 #if $par_regions_bed 18 #if $par_regions_bed
15 && ln -s '${par_regions_bed}' par_regions.bed 19 && ln -s '${par_regions_bed}' par_regions.bed
27 #set $ref_genome = $reference_genome.index.fields.path 31 #set $ref_genome = $reference_genome.index.fields.path
28 #end if 32 #end if
29 && run_deepvariant 33 && run_deepvariant
30 --model_type=$model_type 34 --model_type=$model_type
31 --ref=$ref_genome 35 --ref=$ref_genome
32 --reads='reads_alignment.bam' 36 --reads='reads_alignment.$reads.ext'
33 #if $sample_name 37 #if $sample_name
34 --sample_name '$sample_name' 38 --sample_name '$sample_name'
35 #end if 39 #end if
36 --output_vcf='./output.vcf.gz' 40 --output_vcf='./output.vcf.gz'
37 #if $output_gvcf 41 #if $output_gvcf
88 </when> 92 </when>
89 <when value="history"> 93 <when value="history">
90 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" /> 94 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
91 </when> 95 </when>
92 </conditional> 96 </conditional>
93 <param argument="--reads" type="data" format="bam" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" /> 97 <param argument="--reads" type="data" format="bam,cram" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" />
94 <param argument="--sample_name" type="text" optional="true" label="Sample name" help="Sample name to use instead of the SM tag in the BAM header. Example: NA12878" /> 98 <param argument="--sample_name" type="text" optional="true" label="Sample name" help="Sample name to use instead of the SM tag in the BAM header. Example: NA12878" />
95 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling"> 99 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling">
96 <option value="WGS">WGS: Illumina whole genome sequencing</option> 100 <option value="WGS">WGS: Illumina whole genome sequencing</option>
97 <option value="WES">WES: Illumina whole exome sequencing</option> 101 <option value="WES">WES: Illumina whole exome sequencing</option>
98 <option value="PACBIO">PacBio HiFi</option> 102 <option value="PACBIO">PacBio HiFi</option>
153 <test expect_num_outputs="2"> 157 <test expect_num_outputs="2">
154 <conditional name="reference_genome"> 158 <conditional name="reference_genome">
155 <param name="source" value="history"/> 159 <param name="source" value="history"/>
156 <param name="history_item" value="reference.fasta"/> 160 <param name="history_item" value="reference.fasta"/>
157 </conditional> 161 </conditional>
158 <param name="reads" value="reads.bam"/> 162 <param name="reads" value="reads.bam" ftype="bam"/>
159 <param name="model_type" value="WGS"/> 163 <param name="model_type" value="WGS"/>
160 <param name="output_gvcf" value="False"/> 164 <param name="output_gvcf" value="False"/>
161 <conditional name="regions_conditional"> 165 <conditional name="regions_conditional">
162 <param name="regions_option" value="disabled"/> 166 <param name="regions_option" value="disabled"/>
163 </conditional> 167 </conditional>
183 <test expect_num_outputs="2"> 187 <test expect_num_outputs="2">
184 <conditional name="reference_genome"> 188 <conditional name="reference_genome">
185 <param name="source" value="history"/> 189 <param name="source" value="history"/>
186 <param name="history_item" value="reference.fasta"/> 190 <param name="history_item" value="reference.fasta"/>
187 </conditional> 191 </conditional>
188 <param name="reads" value="reads.bam"/> 192 <param name="reads" value="reads.bam" ftype="bam"/>
189 <param name="model_type" value="WGS"/> 193 <param name="model_type" value="WGS"/>
190 <conditional name="regions_conditional"> 194 <conditional name="regions_conditional">
191 <param name="regions_option" value="region"/> 195 <param name="regions_option" value="region"/>
192 <param name="region_literal" value="K03455:1-2669"/> 196 <param name="region_literal" value="K03455:1-2669"/>
193 </conditional> 197 </conditional>
212 <test expect_num_outputs="2"> 216 <test expect_num_outputs="2">
213 <conditional name="reference_genome"> 217 <conditional name="reference_genome">
214 <param name="source" value="history"/> 218 <param name="source" value="history"/>
215 <param name="history_item" value="reference.fasta"/> 219 <param name="history_item" value="reference.fasta"/>
216 </conditional> 220 </conditional>
217 <param name="reads" value="reads.bam"/> 221 <param name="reads" value="reads.bam" ftype="bam"/>
218 <param name="model_type" value="WGS"/> 222 <param name="model_type" value="WGS"/>
219 <conditional name="regions_conditional"> 223 <conditional name="regions_conditional">
220 <param name="regions_option" value="bed"/> 224 <param name="regions_option" value="bed"/>
221 <param name="bed_file" value="region.bed" ftype="bed"/> 225 <param name="bed_file" value="region.bed" ftype="bed"/>
222 </conditional> 226 </conditional>
241 <test expect_num_outputs="3"> 245 <test expect_num_outputs="3">
242 <conditional name="reference_genome"> 246 <conditional name="reference_genome">
243 <param name="source" value="history"/> 247 <param name="source" value="history"/>
244 <param name="history_item" value="reference.fasta"/> 248 <param name="history_item" value="reference.fasta"/>
245 </conditional> 249 </conditional>
246 <param name="reads" value="reads.bam"/> 250 <param name="reads" value="reads.bam" ftype="bam"/>
247 <param name="model_type" value="WGS"/> 251 <param name="model_type" value="WGS"/>
248 <param name="output_gvcf" value="True"/> 252 <param name="output_gvcf" value="True"/>
249 <conditional name="regions_conditional"> 253 <conditional name="regions_conditional">
250 <param name="regions_option" value="region"/> 254 <param name="regions_option" value="region"/>
251 <param name="region_literal" value="K03455:1-2669"/> 255 <param name="region_literal" value="K03455:1-2669"/>
277 <test expect_num_outputs="2"> 281 <test expect_num_outputs="2">
278 <conditional name="reference_genome"> 282 <conditional name="reference_genome">
279 <param name="source" value="history"/> 283 <param name="source" value="history"/>
280 <param name="history_item" value="reference.fasta"/> 284 <param name="history_item" value="reference.fasta"/>
281 </conditional> 285 </conditional>
282 <param name="reads" value="reads.cram"/> 286 <param name="reads" value="reads.cram" ftype="cram"/>
283 <param name="model_type" value="WGS"/> 287 <param name="model_type" value="WGS"/>
284 <conditional name="regions_conditional"> 288 <conditional name="regions_conditional">
285 <param name="regions_option" value="disabled"/> 289 <param name="regions_option" value="disabled"/>
286 </conditional> 290 </conditional>
287 <section name="advanced_options"> 291 <section name="advanced_options">
305 <test expect_num_outputs="2"> 309 <test expect_num_outputs="2">
306 <conditional name="reference_genome"> 310 <conditional name="reference_genome">
307 <param name="source" value="indexed"/> 311 <param name="source" value="indexed"/>
308 <param name="index" value="phix174"/> 312 <param name="index" value="phix174"/>
309 </conditional> 313 </conditional>
310 <param name="reads" value="reads.bam"/> 314 <param name="reads" value="reads.bam" ftype="bam"/>
311 <param name="model_type" value="WGS"/> 315 <param name="model_type" value="WGS"/>
312 <conditional name="regions_conditional"> 316 <conditional name="regions_conditional">
313 <param name="regions_option" value="disabled"/> 317 <param name="regions_option" value="disabled"/>
314 </conditional> 318 </conditional>
315 <section name="advanced_options"> 319 <section name="advanced_options">
333 <test expect_num_outputs="3"> 337 <test expect_num_outputs="3">
334 <conditional name="reference_genome"> 338 <conditional name="reference_genome">
335 <param name="source" value="history"/> 339 <param name="source" value="history"/>
336 <param name="history_item" value="reference.fasta"/> 340 <param name="history_item" value="reference.fasta"/>
337 </conditional> 341 </conditional>
338 <param name="reads" value="reads.bam"/> 342 <param name="reads" value="reads.bam" ftype="bam"/>
339 <param name="model_type" value="WGS"/> 343 <param name="model_type" value="WGS"/>
340 <conditional name="regions_conditional"> 344 <conditional name="regions_conditional">
341 <param name="regions_option" value="disabled"/> 345 <param name="regions_option" value="disabled"/>
342 </conditional> 346 </conditional>
343 <section name="advanced_options"> 347 <section name="advanced_options">
368 <test expect_num_outputs="2"> 372 <test expect_num_outputs="2">
369 <conditional name="reference_genome"> 373 <conditional name="reference_genome">
370 <param name="source" value="history"/> 374 <param name="source" value="history"/>
371 <param name="history_item" value="reference.fasta"/> 375 <param name="history_item" value="reference.fasta"/>
372 </conditional> 376 </conditional>
373 <param name="reads" value="reads.bam"/> 377 <param name="reads" value="reads.bam" ftype="bam"/>
374 <param name="model_type" value="WGS"/> 378 <param name="model_type" value="WGS"/>
375 <conditional name="regions_conditional"> 379 <conditional name="regions_conditional">
376 <param name="regions_option" value="disabled"/> 380 <param name="regions_option" value="disabled"/>
377 </conditional> 381 </conditional>
378 <section name="advanced_options"> 382 <section name="advanced_options">
398 <test expect_num_outputs="2"> 402 <test expect_num_outputs="2">
399 <conditional name="reference_genome"> 403 <conditional name="reference_genome">
400 <param name="source" value="history"/> 404 <param name="source" value="history"/>
401 <param name="history_item" value="reference.fasta"/> 405 <param name="history_item" value="reference.fasta"/>
402 </conditional> 406 </conditional>
403 <param name="reads" value="reads.bam"/> 407 <param name="reads" value="reads.bam" ftype="bam"/>
404 <param name="model_type" value="WGS"/> 408 <param name="model_type" value="WGS"/>
405 <conditional name="regions_conditional"> 409 <conditional name="regions_conditional">
406 <param name="regions_option" value="disabled"/> 410 <param name="regions_option" value="disabled"/>
407 </conditional> 411 </conditional>
408 <section name="advanced_options"> 412 <section name="advanced_options">