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comparison bwa-mem.xml @ 24:64f11cf59c6e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 055c6c3de6c9e0f219f5792f6580244815c1cd31"
author iuc
date Wed, 05 May 2021 18:22:08 +0000
parents 3fe632431b68
children e188dc7a68e6
comparison
equal deleted inserted replaced
23:3fe632431b68 24:64f11cf59c6e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.1"> 2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2">
3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description> 3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
4 <macros> 4 <macros>
5 <import>read_group_macros.xml</import> 5 <import>read_group_macros.xml</import>
6 <import>bwa_macros.xml</import> 6 <import>bwa_macros.xml</import>
7 </macros> 7 </macros>
12 @set_reference_fasta_filename@ 12 @set_reference_fasta_filename@
13 13
14 ## Begin BWA-MEM command line 14 ## Begin BWA-MEM command line
15 15
16 bwa mem 16 bwa mem
17 -t "\${GALAXY_SLOTS:-1}" 17
18 #if str( $output_sort ) == "unsorted":
19 -t 1
20 #else
21 -t "\${GALAXY_SLOTS:-1}"
22 #end if
18 ## Verbosity is set to 1 (errors only) 23 ## Verbosity is set to 1 (errors only)
19 -v 1 24 -v 1
20 25
21 #if str( $fastq_input.fastq_input_selector ) == "paired_iv": 26 #if str( $fastq_input.fastq_input_selector ) == "paired_iv":
22 ## For interleaved fastq files set -p option 27 ## For interleaved fastq files set -p option
104 #else: 109 #else:
105 '${reference_fasta_filename}' 110 '${reference_fasta_filename}'
106 '${fastq_input.fastq_input1}' 111 '${fastq_input.fastq_input1}'
107 #end if 112 #end if
108 113
109 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output' 114 #if str( $output_sort ) == "coordinate":
115 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
116 #elif str( $output_sort ) == "name":
117 | samtools sort -n -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
118 #else
119 | samtools view -@ \${GALAXY_SLOTS:-2} -bS - -o '$bam_output'
120 #end if
121
122
110 ]]></command> 123 ]]></command>
111 124
112 <inputs> 125 <inputs>
113 <expand macro="reference_source_conditional" /> 126 <expand macro="reference_source_conditional" />
114 <conditional name="fastq_input"> 127 <conditional name="fastq_input">
245 <!-- do nothing --> 258 <!-- do nothing -->
246 </when> 259 </when>
247 </conditional> 260 </conditional>
248 </when> 261 </when>
249 </conditional> 262 </conditional>
263 <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can extend the run time of the tool significantly (cause it requires running on only a single thread).">
264 <option value="coordinate" selected="True">Sort by chromosomal coordinates</option>
265 <option value="name">Sort by read names (i.e., the QNAME field) </option>
266 <option value="unsorted">Not sorted (sorted as input)</option>
267 </param>
250 </inputs> 268 </inputs>
251 269
252 <outputs> 270 <outputs>
253 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"> 271 <data format="bam" name="bam_output" label="${tool.name} on ${on_string} (mapped reads in BAM format)">
254 <expand macro="dbKeyActionsBwaMem" /> 272 <expand macro="dbKeyActionsBwaMem" />
273 <change_format>
274 <when input="output_sort" value="name" format="qname_sorted.bam" />
275 <when input="output_sort" value="unsorted" format="qname_input_sorted.bam" />
276 </change_format>
255 </data> 277 </data>
256 </outputs> 278 </outputs>
257 279
258 <tests> 280 <tests>
259 <test> 281 <test>
294 <param name="PL" value="CAPILLARY"/> 316 <param name="PL" value="CAPILLARY"/>
295 <param name="LB" value="AARDVARK-1" /> 317 <param name="LB" value="AARDVARK-1" />
296 <param name="analysis_type_selector" value="illumina"/> 318 <param name="analysis_type_selector" value="illumina"/>
297 <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="2" /> 319 <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="2" />
298 </test> 320 </test>
321 <test>
322 <param name="reference_source_selector" value="history" />
323 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
324 <param name="fastq_input_selector" value="paired"/>
325 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
326 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
327 <param name="analysis_type_selector" value="illumina"/>
328 <param name="output_sort" value="unsorted"/>
329 <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="2" />
330 </test>
331 <test>
332 <param name="reference_source_selector" value="history" />
333 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
334 <param name="fastq_input_selector" value="paired"/>
335 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
336 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
337 <param name="analysis_type_selector" value="illumina"/>
338 <param name="output_sort" value="name"/>
339 <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="2" />
340 </test>
299 </tests> 341 </tests>
300 <help><![CDATA[ 342 <help><![CDATA[
301 **What is does** 343 **What is does**
302 344
303 From http://arxiv.org/abs/1303.3997: 345 From http://arxiv.org/abs/1303.3997:
329 Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are: 371 Galaxy allows four levels of control over bwa-mem options provided by **Select analysis mode** menu option. These are:
330 372
331 1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2] 373 1. *Simple Illumina mode*: The simplest possible bwa mem application in which it alignes single or paired-end data to reference using default parameters. It is equivalent to the following command: bwa mem <reference index> <fastq dataset1> [fastq dataset2]
332 2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 <reference index> <PacBio dataset in fastq format> 374 2. *PacBio mode*: The mode adjusted specifically for mapping of long PacBio subreads. Equivalent to the following command: bwa mem -k17 -W40 -r10 -A1 -B1 -O1 -E1 -L0 <reference index> <PacBio dataset in fastq format>
333 3. *Full list of options*: Allows access to all options through Galaxy interface. 375 3. *Full list of options*: Allows access to all options through Galaxy interface.
376
377 -----
378
379 **Bam sorting mode**
380
381 The generated bam files can be sorted according to three criteria: coordinates, names and input order.
382
383 In coordinate sorted mode the reads are sorted by coordinates. It means that the reads from the beginning of the first chromosome are first in the file.
384
385 When sorted by read name, the file is sorted by the reference ID (i.e., the QNAME field).
386
387 Finally, the *No sorted (sorted as input)* option yield a BAM file in which the records are sorted in an order corresponding to the order of the reads in the original input file. This option requires using a single thread to perform the conversion from SAM to BAM format, so the runtime is extended.
388
334 389
335 @RG@ 390 @RG@
336 391
337 @info@ 392 @info@
338 ]]></help> 393 ]]></help>