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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 6e9628b1d92fdb358b79959ad54a456cfa46fa33
author iuc
date Fri, 17 May 2024 21:09:07 +0000
parents e188dc7a68e6
children
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25:e188dc7a68e6 26:2477830927ec
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa" name="Map with BWA" version="@VERSION@.5"> 2 <tool id="bwa" name="Map with BWA" version="@TOOL_VERSION@" profile="22.05">
3 <description>- map short reads (&lt; 100 bp) against reference genome</description> 3 <description>- map short reads (&lt; 100 bp) against reference genome</description>
4 <xrefs>
5 <xref type="bio.tools">bwa</xref>
6 </xrefs>
7 <macros> 4 <macros>
8 <import>read_group_macros.xml</import> 5 <import>read_group_macros.xml</import>
9 <import>bwa_macros.xml</import> 6 <import>bwa_macros.xml</import>
10 <token name="@command_options@"> 7 <token name="@command_options@">
11 #if str( $analysis_type.analysis_type_selector ) == "full": 8 #if str( $analysis_type.analysis_type_selector ) == "full":
75 <when value="do_not_set"> 72 <when value="do_not_set">
76 <!-- do nothing --> 73 <!-- do nothing -->
77 </when> 74 </when>
78 </xml> 75 </xml>
79 </macros> 76 </macros>
77 <expand macro="bio_tools"/>
80 <expand macro="requirements"/> 78 <expand macro="requirements"/>
81 <expand macro="stdio"/> 79 <expand macro="stdio"/>
82 <command> 80 <command>
83 <![CDATA[ 81 <![CDATA[
84 @pipefail@ 82 @pipefail@
312 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"> 310 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
313 <expand macro="dbKeyActionsBwaMem"/> 311 <expand macro="dbKeyActionsBwaMem"/>
314 </data> 312 </data>
315 </outputs> 313 </outputs>
316 <tests> 314 <tests>
317 <test> 315 <!-- `samtools sort` in the new update adds PG lines to the output so the lines_diff is changed from "2" to "4" -->
316 <test expect_num_outputs="1">
318 <param name="reference_source_selector" value="history"/> 317 <param name="reference_source_selector" value="history"/>
319 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 318 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
320 <param name="input_type_selector" value="single"/> 319 <param name="input_type_selector" value="single"/>
321 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/> 320 <param name="fastq_input1" ftype="fasta" value="bwa-mem-fasta1.fa"/>
322 <param name="analysis_type_selector" value="illumina"/> 321 <param name="analysis_type_selector" value="illumina"/>
323 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="2"/> 322 <output name="bam_output" ftype="bam" file="bwa-aln-test1-fasta.bam" lines_diff="4"/>
324 </test> 323 </test>
325 <test> 324 <test expect_num_outputs="1">
326 <param name="reference_source_selector" value="history"/> 325 <param name="reference_source_selector" value="history"/>
327 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 326 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
328 <param name="input_type_selector" value="paired"/> 327 <param name="input_type_selector" value="paired"/>
329 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> 328 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
330 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 329 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
331 <param name="analysis_type_selector" value="illumina"/> 330 <param name="analysis_type_selector" value="illumina"/>
332 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/> 331 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="4"/>
333 </test> 332 </test>
334 <test> 333 <test expect_num_outputs="1">
335 <param name="reference_source_selector" value="history"/> 334 <param name="reference_source_selector" value="history"/>
336 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 335 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
337 <param name="input_type_selector" value="paired"/> 336 <param name="input_type_selector" value="paired"/>
338 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> 337 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
339 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 338 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
340 <param name="analysis_type_selector" value="illumina"/> 339 <param name="analysis_type_selector" value="illumina"/>
341 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="2"/> 340 <output name="bam_output" ftype="bam" file="bwa-aln-test1.bam" lines_diff="4"/>
342 </test> 341 </test>
343 <test> 342 <test expect_num_outputs="1">
344 <param name="reference_source_selector" value="history"/> 343 <param name="reference_source_selector" value="history"/>
345 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 344 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
346 <param name="input_type_selector" value="paired_bam"/> 345 <param name="input_type_selector" value="paired_bam"/>
347 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/> 346 <param name="bam_input" ftype="bam" value="bwa-aln-bam-input.bam"/>
348 <param name="analysis_type_selector" value="illumina"/> 347 <param name="analysis_type_selector" value="illumina"/>
349 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="2"/> 348 <output name="bam_output" ftype="bam" file="bwa-aln-test2.bam" lines_diff="4"/>
350 </test> 349 </test>
351 <test> 350 <test expect_num_outputs="1">
352 <param name="reference_source_selector" value="history"/> 351 <param name="reference_source_selector" value="history"/>
353 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 352 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
354 <param name="input_type_selector" value="paired"/> 353 <param name="input_type_selector" value="paired"/>
355 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> 354 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
356 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 355 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
357 <param name="rg_selector" value="set"/> 356 <param name="rg_selector" value="set"/>
358 <param name="ID" value="rg1"/> 357 <param name="ID" value="rg1"/>
359 <param name="PL" value="CAPILLARY"/> 358 <param name="PL" value="CAPILLARY"/>
360 <param name="analysis_type_selector" value="illumina"/> 359 <param name="analysis_type_selector" value="illumina"/>
361 <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="2"/> 360 <output name="bam_output" ftype="bam" file="bwa-aln-test3.bam" lines_diff="5"/>
362 </test> 361 </test>
363 </tests> 362 </tests>
364 <help><![CDATA[ 363 <help><![CDATA[
365 **What is does** 364 **What it does**
366 365
367 BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the 366 BWA_ is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
368 human genome. The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use 367 The bwa-aln algorithm is designed for Illumina sequence reads up to 100bp. For longer reads use the separate BWA-MEM Galaxy tool.
369 the separate BWA-MEM Galaxy tool. 368
370 369 This Galaxy tool wraps the bwa-aln, bwa-samse and -sampe modules of the BWA read mapping tool:
371 This Galaxy tool wraps bwa-aln, bwa-samse and -sampe modules of bwa read mapping tool:
372 370
373 - **bwa aln** - actual mapper placing reads onto the reference sequence 371 - **bwa aln** - actual mapper placing reads onto the reference sequence
374 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for 372 - **bwa samse** - post-processor converting suffix array coordinates into genome coordinates in SAM format for
375 single reads 373 single reads
376 - **bam sampe** - post-processor for paired reads 374 - **bam sampe** - post-processor for paired reads
377 375
376 For more details about the different modules of the BWA package see the `BWA manual`_.
378 377
379 The Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM format, 378 The Galaxy implementation takes fastq or BAM (unaligned BAM) datasets as input and produces output in BAM format,
380 which can be further processed using various BAM utilities exiting in Galaxy (BAMTools, SAMTools, Picard). 379 which can be further processed using various BAM utilities existing in Galaxy (BAMTools, SAMTools, Picard).
381 380
382 ----- 381 -----
383 382
384 **Indices: Selecting reference genomes for BWA** 383 @ref_genomes@
385
386 The Galaxy wrapper for BWA allows you to select between precomputed and user-defined indices for reference genomes
387 using the **Will you select a reference genome from your history or use a built-in index?** select box.
388
389 This select box has two options:
390
391 1. **Use a built-in genome index** - when selected (this is default), Galaxy provides the user with **Select
392 reference genome index** dropdown. Genomes listed in this dropdown have been pre-indexed with bwa index utility
393 and are ready to be mapped against.
394 2. **Use a genome from the history and build index** - when selected, Galaxy provides the user with **Select
395 reference genome sequence** dropdown. This dropdown is populated by all FASTA formatted files listed in your
396 current history. If your genome of interest is uploaded into history it will be shown there. Selecting a genome
397 from this dropdown will cause Galaxy to first transparently index it using `bwa index` command, and then run
398 mapping with `bwa aln`.
399
400
401 If your genome of interest is not listed here you have two choices:
402
403 1. Contact galaxy team using **Help->Support** link at the top of the interface and let us know that an index
404 needs to be added
405 2. Upload your genome of interest as a FASTA file to Galaxy history and selected **Use a genome from the history
406 and build index** option.
407
408 384
409 @RG@ 385 @RG@
410 386
411 @info@ 387 @links@
412 ]]></help> 388 ]]></help>
413 <citations> 389 <citations>
414 <citation type="doi">10.1093/bioinformatics/btp324</citation> 390 <citation type="doi">10.1093/bioinformatics/btp324</citation>
415 <citation type="doi">10.1093/bioinformatics/btp698</citation> 391 <citation type="doi">10.1093/bioinformatics/btp698</citation>
416 </citations> 392 </citations>