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comparison winnowmap.xml @ 2:ff38e5f728ce draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/winnowmap commit f12e139eb362fea66360aefbbc678197e2440139"
author iuc
date Tue, 13 Jul 2021 12:15:48 +0000
parents ffde24d658e9
children
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1:49723fdb9683 2:ff38e5f728ce
1 <tool id="winnowmap" name="Winnowmap" version="@TOOL_VERSION@+galaxy0" profile="20.01"> 1 <tool id="winnowmap" name="Winnowmap" version="@TOOL_VERSION@+galaxy1" profile="20.05">
2 <description>a mapping tool optimized for repetitive sequences</description> 2 <description>a mapping tool optimized for repetitive sequences</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="edam_ontology"/> 6 <expand macro="edam_ontology"/>
143 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse' 143 '$fastq_input.fastq_input1.forward' '$fastq_input.fastq_input1.reverse'
144 #end if 144 #end if
145 #if $io_options.output_format == 'BAM': 145 #if $io_options.output_format == 'BAM':
146 -a 146 -a
147 | samtools sort 147 | samtools sort
148 --no-PG
148 -@\${GALAXY_SLOTS:-2} 149 -@\${GALAXY_SLOTS:-2}
149 -T "\${TMPDIR:-.}" 150 -T "\${TMPDIR:-.}"
150 -O $io_options.output_format 151 -O $io_options.output_format
151 -o '$alignment_output' 152 -o '$alignment_output'
152 #else if $io_options.output_format == 'CRAM': 153 #else if $io_options.output_format == 'CRAM':
153 -a 154 -a
154 | samtools sort 155 | samtools sort
156 --no-PG
155 -T "\${TMPDIR:-.}" 157 -T "\${TMPDIR:-.}"
156 -@\${GALAXY_SLOTS:-2} 158 -@\${GALAXY_SLOTS:-2}
157 -O $io_options.output_format 159 -O $io_options.output_format
158 $io_options.eqx 160 $io_options.eqx
159 --reference reference.fa 161 --reference reference.fa
227 <param argument="-k" type="integer" min="4" max="28" optional="true" label="K-mer size" help="k-mer size (no larger than 28). "/> 229 <param argument="-k" type="integer" min="4" max="28" optional="true" label="K-mer size" help="k-mer size (no larger than 28). "/>
228 <param argument="-w" type="integer" min="1" optional="true" label="Minimizer window size" help=""/> 230 <param argument="-w" type="integer" min="1" optional="true" label="Minimizer window size" help=""/>
229 <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/> 231 <param argument="-I" type="integer" min="1" optional="true" label="Split index for every N input gigabases" help=""/>
230 </section> 232 </section>
231 <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, --sv-off and --min-occ-floor options." expanded="False"> 233 <section name="mapping_options" title="Mapping options" help="Sets -f, -g, -F, -r, -n, -m, -X, -p, --sv-off and --min-occ-floor options." expanded="False">
232 <param name="sv_off" argument="--sv-off" type="boolean" truevalue="--sv-off" falsevalue="" checked="False" label="Turn off SV-aware mode" help="SV aware k-mer search allows to find approximate mapping locations for a read"/> 234 <param argument="--sv-off" type="boolean" truevalue="--sv-off" falsevalue="" checked="False" label="Turn off SV-aware mode" help="SV aware k-mer search allows to find approximate mapping locations for a read"/>
233 <param argument="-F" type="integer" min="0" value="" optional="true" 235 <param argument="-F" type="integer" min="0" value="" optional="true"
234 label="Max fragment length for PE alignment" 236 label="Max fragment length for PE alignment"
235 help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" /> 237 help="The maximum apparent fragment length up to which paired-end reads are aligned together; at higher fragment lengths the mates will be aligned independent of each other; effective only for paired-end data and when spliced alignment mode is turned off; default=800" />
236 <param argument="-f" type="float" value="" optional="true" label="Filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/> 238 <param argument="-f" type="float" value="" optional="true" label="Filter out top FLOAT fraction of repetitive minimizers" help="default=0.0002"/>
237 <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="Force winnowmap to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" /> 239 <param argument="--min-occ-floor" name="min_occ_floor" type="integer" label="Force winnowmap to always use k-mers occuring this many times or fewer" help="Maximum occurence is the number of repetitive minimizers determined by '-f' or this value, whichever is higher." optional="true" />
359 </action> 361 </action>
360 </when> 362 </when>
361 </conditional> 363 </conditional>
362 </actions> 364 </actions>
363 <change_format> 365 <change_format>
364 <when input="io_options.output_format" value="paf" format="tabular" /> 366 <when input="io_options.output_format" value="paf" format="paf" />
365 <when input="io_options.output_format" value="CRAM" format="cram" /> 367 <when input="io_options.output_format" value="CRAM" format="cram" />
366 </change_format> 368 </change_format>
367 </data> 369 </data>
368 </outputs> 370 </outputs>
369 <tests> 371 <tests>
373 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 375 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
374 <param name="fastq_input_selector" value="single"/> 376 <param name="fastq_input_selector" value="single"/>
375 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 377 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
376 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> 378 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
377 <param name="analysis_type_selector" value="map-ont"/> 379 <param name="analysis_type_selector" value="map-ont"/>
378 <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" /> 380 <param name="min_occ_floor" value="1000"/>
381 <section name="alignment_options">
382 <param name="min_occ_floor" value="1000"/>
383 <param name="A" value="2"/>
384 <param name="B" value="8"/>
385 <param name="O" value="12"/>
386 <param name="O2" value="32"/>
387 <param name="E" value="2"/>
388 <param name="E2" value="1"/>
389 <param name="z" value="400"/>
390 <param name="s" value="40"/>
391 </section>
392 <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" >
393 <metadata name="dbkey" value="?" />
394 </output>
379 </test> 395 </test>
380 <test> 396 <test>
381 <!-- test cram output --> 397 <!-- test cram output -->
382 <param name="reference_source_selector" value="history" /> 398 <param name="reference_source_selector" value="history" />
383 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 399 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa" dbkey="hg19"/>
384 <param name="fastq_input_selector" value="single"/> 400 <param name="fastq_input_selector" value="single"/>
385 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 401 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
386 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> 402 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
387 <param name="analysis_type_selector" value="map-ont"/> 403 <param name="analysis_type_selector" value="map-ont"/>
388 <param name="output_format" value="CRAM"/> 404 <param name="output_format" value="CRAM"/>
389 <output name="alignment_output" ftype="cram" file="winnowmap-test1-fasta.cram" compare="sim_size" /> 405 <output name="alignment_output" ftype="cram" file="winnowmap-test1-fasta.cram" lines_diff="2">
406 <metadata name="dbkey" value="hg19" />
407 </output>
390 </test> 408 </test>
391 <test> 409 <test>
392 <!-- test paired input --> 410 <!-- test paired input -->
393 <param name="reference_source_selector" value="history" /> 411 <param name="reference_source_selector" value="history" />
394 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 412 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
420 <element name="forward" value="bwa-mem-fastq1.fq" /> 438 <element name="forward" value="bwa-mem-fastq1.fq" />
421 <element name="reverse" value="bwa-mem-fastq2.fq" /> 439 <element name="reverse" value="bwa-mem-fastq2.fq" />
422 </collection> 440 </collection>
423 </param> 441 </param>
424 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> 442 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
425 <output name="alignment_output" ftype="bam" file="winnowmap-test2.bam" lines_diff="2" /> 443 <output name="alignment_output" ftype="bam" file="winnowmap-test2.bam" lines_diff="2"/>
426 </test> 444 </test>
427 <test> 445 <test>
428 <!-- test data table reference --> 446 <!-- test data table reference -->
429 <param name="reference_source_selector" value="cached" /> 447 <param name="reference_source_selector" value="cached" />
430 <param name="ref_file" value="bwa-mem-mt-genome"/> 448 <param name="ref_file" value="bwa-mem-mt-genome" dbkey="hg19"/>
431 <param name="fastq_input_selector" value="single"/> 449 <param name="fastq_input_selector" value="single"/>
432 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/> 450 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
433 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> 451 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
434 <param name="analysis_type_selector" value="map-ont"/> 452 <param name="analysis_type_selector" value="map-ont"/>
435 <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" /> 453 <section name="alignment_options">
454 <param name="min_occ_floor" value="1000"/>
455 <param name="A" value="2"/>
456 <param name="B" value="8"/>
457 <param name="O" value="12"/>
458 <param name="O2" value="32"/>
459 <param name="E" value="2"/>
460 <param name="E2" value="1"/>
461 <param name="z" value="400"/>
462 <param name="s" value="40"/>
463 </section>
464 <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" >
465 <metadata name="dbkey" value="bwa-mem-mt-genome-dbkey" />
466 </output>
436 </test> 467 </test>
437 <test> 468 <test>
438 <!-- test alignment options --> 469 <!-- test alignment options -->
439 <param name="reference_source_selector" value="cached" /> 470 <param name="reference_source_selector" value="cached" />
440 <param name="min_occ_floor" value="1000"/> 471 <param name="min_occ_floor" value="1000"/>
455 <param name="E2" value="1" /> 486 <param name="E2" value="1" />
456 <param name="z" value="400" /> 487 <param name="z" value="400" />
457 <param name="s" value="40" /> 488 <param name="s" value="40" />
458 </section> 489 </section>
459 <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" /> 490 <output name="alignment_output" ftype="bam" file="winnowmap-test1-fasta.bam" lines_diff="2" />
491 <assert_command>
492 <has_text text="-A 2"/>
493 <has_text text="-B 8"/>
494 <has_text text="-O 12,32"/>
495 <has_text text="-E 2,1"/>
496 <has_text text="-z 400"/>
497 <has_text text="-s 40"/>
498 </assert_command>
460 </test> 499 </test>
461 <test> 500 <test>
462 <!-- test paf output --> 501 <!-- test paf output -->
463 <param name="reference_source_selector" value="history" /> 502 <param name="reference_source_selector" value="history" />
464 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" /> 503 <param name="ref_file" ftype="fastqsanger" value="mini_reads.fq" />
465 <param name="fastq_input_selector" value="single"/> 504 <param name="fastq_input_selector" value="single"/>
466 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" /> 505 <param name="fastq_input1" ftype="fastqsanger" value="mini_reads.fq" />
467 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/> 506 <param name="highfreq_kmers" ftype="tabular" value="repetitive_k15.txt"/>
468 <param name="analysis_type_selector" value="map-ont"/> 507 <param name="analysis_type_selector" value="map-ont"/>
469 <param name="output_format" value="paf"/> 508 <param name="output_format" value="paf"/>
470 <output name="alignment_output" ftype="tabular" file="mini_reads.paf" /> 509 <output name="alignment_output" ftype="paf" file="mini_reads.paf" />
471 </test> 510 </test>
472 <test> 511 <test>
473 <!-- test self-homology mode --> 512 <!-- test self-homology mode -->
474 <param name="reference_source_selector" value="history" /> 513 <param name="reference_source_selector" value="history" />
475 <param name="ref_file" ftype="fasta" value="winnowmap-self-homology.fasta" /> 514 <param name="ref_file" ftype="fasta" value="winnowmap-self-homology.fasta" />