Mercurial > repos > iuc > bcftools_mpileup

comparison bcftools_mpileup.xml @ 5:0bf290bc84ae draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 12:56:14 -0400
parents 9a2923126c43
children d1d0defa52af
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4:9a2923126c43 5:0bf290bc84ae
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy2">
3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> 3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">mpileup</token> 5 <token name="@EXECUTABLE@">mpileup</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <xml name="bam_flag_options"> 7 <xml name="bam_flag_options">
289 <when value="no_limit" /> 289 <when value="no_limit" />
290 </conditional> 290 </conditional>
291 </section> 291 </section>
292 292
293 <section name="sec_restrict" expanded="false" title="Restrict to"> 293 <section name="sec_restrict" expanded="false" title="Restrict to">
294 <expand macro="macro_regions" /> 294 <expand macro="macro_restrict" />
295 <expand macro="macro_targets" /> 295 <expand macro="macro_restrict" type="target" label_type="Target">
296 <expand macro="macro_invert_targets" />
297 </expand>
296 </section> 298 </section>
297 <section name="sec_subset" expanded="false" title="Subset Options"> 299 <section name="sec_subset" expanded="false" title="Subset Options">
298 <expand macro="macro_samples" /> 300 <expand macro="macro_samples" />
299 </section> 301 </section>
300 302
344 </output> 346 </output>
345 </test> 347 </test>
346 <test> 348 <test>
347 <param name="input_number" value="single" /> 349 <param name="input_number" value="single" />
348 <param name="input_bam" ftype="bam" value="mpileup.1.bam" /> 350 <param name="input_bam" ftype="bam" value="mpileup.1.bam" />
349 <param name="reference_source_selector" value="history" /> 351 <param name="reference_source_selector" value="cached" />
350 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 352 <param name="ref_file" value="mpileup" />
351 <param name="quality_settings" value="adjust" /> 353 <param name="quality_settings" value="adjust" />
352 <param name="output_type" value="v" /> 354 <param name="output_type" value="v" />
353 <output name="output_file"> 355 <output name="output_file">
354 <assert_contents> 356 <assert_contents>
355 <has_text text="mpileup" /> 357 <has_text text="mpileup" />
376 <test> 378 <test>
377 <param name="input_number" value="multiple" /> 379 <param name="input_number" value="multiple" />
378 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" /> 380 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
379 <param name="reference_source_selector" value="history" /> 381 <param name="reference_source_selector" value="history" />
380 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 382 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
381 <param name="regions_src" value="regions" /> 383 <section name="sec_restrict">
382 <param name="regions" value="17:100-110" /> 384 <conditional name="regions">
385 <param name="regions_src" value="regions" />
386 <repeat name="regions">
387 <param name="chrom" value="17" />
388 <param name="start" value="100" />
389 <param name="stop" value="110" />
390 </repeat>
391 </conditional>
392 </section>
383 <param name="output_tags" value="DP,INFO/AD,DV" /> 393 <param name="output_tags" value="DP,INFO/AD,DV" />
384 <param name="output_type" value="v" /> 394 <param name="output_type" value="v" />
385 <output name="output_file"> 395 <output name="output_file">
386 <assert_contents> 396 <assert_contents>
387 <has_text text="mpileup" /> 397 <has_text text="mpileup" />
397 <test> 407 <test>
398 <param name="input_number" value="multiple" /> 408 <param name="input_number" value="multiple" />
399 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" /> 409 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
400 <param name="reference_source_selector" value="history" /> 410 <param name="reference_source_selector" value="history" />
401 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 411 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
402 <param name="regions_src" value="regions_file" /> 412 <section name="sec_restrict">
403 <param name="regions_file" ftype="bed" value="mpileup.regions.bed" /> 413 <conditional name="targets">
404 <param name="targets_src" value="targets" /> 414 <param name="targets_src" value="targets" />
405 <param name="targets" value="17:100-104" /> 415 <repeat name="targets">
416 <param name="chrom" value="17" />
417 <param name="start" value="100" />
418 <param name="stop" value="104" />
419 </repeat>
420 </conditional>
421 </section>
406 <param name="output_tags" value="DP,INFO/AD,DV" /> 422 <param name="output_tags" value="DP,INFO/AD,DV" />
407 <param name="output_type" value="v" /> 423 <param name="output_type" value="v" />
408 <output name="output_file"> 424 <output name="output_file">
409 <assert_contents> 425 <assert_contents>
410 <has_text text="mpileup" /> 426 <has_text text="mpileup" />
420 <test> 436 <test>
421 <param name="input_number" value="multiple" /> 437 <param name="input_number" value="multiple" />
422 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" /> 438 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
423 <param name="reference_source_selector" value="history" /> 439 <param name="reference_source_selector" value="history" />
424 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> 440 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
425 <param name="regions_src" value="regions" /> 441 <section name="sec_restrict">
426 <param name="regions" value="17:1050-1060" /> 442 <conditional name="regions">
443 <param name="regions_src" value="regions" />
444 <repeat name="regions">
445 <param name="chrom" value="17" />
446 <param name="start" value="1050" />
447 <param name="stop" value="1060" />
448 </repeat>
449 </conditional>
450 </section>
427 <param name="filter_flags" value="filter" /> 451 <param name="filter_flags" value="filter" />
428 <param name="exclude_flags" value="4,16" /> 452 <param name="exclude_flags" value="4,16" />
429 <param name="output_type" value="v" /> 453 <param name="output_type" value="v" />
430 <output name="output_file"> 454 <output name="output_file">
431 <assert_contents> 455 <assert_contents>