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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit ed3c07cc67bacb7c1c5a929d5f427536a35db5ca
author iuc
date Mon, 24 Mar 2025 18:10:21 +0000
parents 170061c052ad
children
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21:170061c052ad 22:5d365d5cbe9d
1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description> 2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.24.0</token> 4 <token name="@TOOL_VERSION@">0.25.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> 6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
7 <xml name="reads"> 7 <xml name="reads">
8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads"/> 8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads"/>
9 </xml> 9 </xml>
70 #set $hap1_filenames = $mode.trioinput.hap1_list 70 #set $hap1_filenames = $mode.trioinput.hap1_list
71 #set $hap2_filenames = $mode.trioinput.hap2_list 71 #set $hap2_filenames = $mode.trioinput.hap2_list
72 #end if 72 #end if
73 #end if 73 #end if
74 hifiasm 74 hifiasm
75 #if str($mode.mode_selector) == 'ont':
76 --ont
77 #end if
75 -t \${GALAXY_SLOTS:-1} 78 -t \${GALAXY_SLOTS:-1}
76 -o output 79 -o output
77 -f $filter_bits 80 -f $filter_bits
78 #if str($advanced_options.advanced_selector) == 'set': 81 #if str($advanced_options.advanced_selector) == 'set':
79 -k $advanced_options.hifiasm_kmer_length 82 -k $advanced_options.hifiasm_kmer_length
86 #end if 89 #end if
87 --max-kocc $advanced_options.max_kocc 90 --max-kocc $advanced_options.max_kocc
88 #if $advanced_options.hg_size 91 #if $advanced_options.hg_size
89 --hg-size $advanced_options.hg_size 92 --hg-size $advanced_options.hg_size
90 #end if 93 #end if
94 --rl-cut $advanced_options.rl_cut
95 --sc-cut $advanced_options.sc_cut
91 96
92 #end if 97 #end if
93 #if str($assembly_options.assembly_selector) == 'set': 98 #if str($assembly_options.assembly_selector) == 'set':
94 -a $assembly_options.cleaning_rounds 99 -a $assembly_options.cleaning_rounds
95 -z $assembly_options.adapter_length 100 -z $assembly_options.adapter_length
179 </command> 184 </command>
180 <inputs> 185 <inputs>
181 <conditional name="mode"> 186 <conditional name="mode">
182 <param name="mode_selector" type="select" label="Assembly mode"> 187 <param name="mode_selector" type="select" label="Assembly mode">
183 <option value="standard">Standard</option> 188 <option value="standard">Standard</option>
189 <option value="ont">ONT</option>
184 <option value="trio">Trio mode</option> 190 <option value="trio">Trio mode</option>
185 </param> 191 </param>
186 <when value="standard"> 192 <when value="standard">
193 <expand macro="reads"/>
194 </when>
195 <when value="ont">
187 <expand macro="reads"/> 196 <expand macro="reads"/>
188 </when> 197 </when>
189 <when value="trio"> 198 <when value="trio">
190 <expand macro="reads"/> 199 <expand macro="reads"/>
191 <conditional name="trioinput"> 200 <conditional name="trioinput">
301 <add value="g"/> 310 <add value="g"/>
302 </valid> 311 </valid>
303 </sanitizer> 312 </sanitizer>
304 <validator type="regex">[0-9kKmMGg]+</validator> 313 <validator type="regex">[0-9kKmMGg]+</validator>
305 </param> 314 </param>
315 <param argument="--rl-cut" type="integer" min="0" value="1000" optional="true" label="ONT Read length cutoff" help="Filter out ONT simplex reads shorter than specified length for assembly"/>
316 <param argument="--sc-cut" type="integer" min="0" value="10" optional="true" label="ONT Base Quality Score cutoff" help="Filter out ONT simplex reads with mean base quality score specified value for assembly"/>
306 </when> 317 </when>
307 </conditional> 318 </conditional>
308 <conditional name="scaffolding_options"> 319 <conditional name="scaffolding_options">
309 <param name="scaffold_selector" type="select" label="Options for hifiasm scaffolding"> 320 <param name="scaffold_selector" type="select" label="Options for hifiasm scaffolding">
310 <option value="blank">No scaffolding (default)</option> 321 <option value="blank">No scaffolding (default)</option>
317 </conditional> 328 </conditional>
318 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/> 329 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
319 <param name="bins_out" type="boolean" label="Output .bin files (used for development and debugging)?" truevalue="yes" falsevalue="no"/> 330 <param name="bins_out" type="boolean" label="Output .bin files (used for development and debugging)?" truevalue="yes" falsevalue="no"/>
320 </inputs> 331 </inputs>
321 <outputs> 332 <outputs>
322 <!--Standard mode--> 333 <!--Standard and ONT mode-->
323 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for pseudohaplotype assembly"> 334 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for pseudohaplotype assembly">
324 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> 335 <filter>mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
325 </data> 336 </data>
326 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph for pseudohaplotype assembly"> 337 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph for pseudohaplotype assembly">
327 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> 338 <filter>mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
328 </data> 339 </data>
329 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph for pseudohaplotype assembly"> 340 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph for pseudohaplotype assembly">
330 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> 341 <filter>mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
331 </data> 342 </data>
332 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph for pseudohaplotype assembly"> 343 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph for pseudohaplotype assembly">
333 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter> 344 <filter>mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
334 </data> 345 </data>
335 <!--Trio outputs without Hi-c reads--> 346 <!--Trio outputs without Hi-c reads-->
336 <data name="hap1_contigs" format="gfa1" from_work_dir="output.dip.hap1.p_ctg.gfa" label="${tool.name} on ${on_string}: hap1.p_ctg contig graph"> 347 <data name="hap1_contigs" format="gfa1" from_work_dir="output.dip.hap1.p_ctg.gfa" label="${tool.name} on ${on_string}: hap1.p_ctg contig graph">
337 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter> 348 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
338 </data> 349 </data>
345 <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph for HiC-phased assembly"> 356 <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph for HiC-phased assembly">
346 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter> 357 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
347 </data> 358 </data>
348 <!-- Stardand mode with Hi-C partition outputs --> 359 <!-- Stardand mode with Hi-C partition outputs -->
349 <data name="hic_pcontig_graph" format="gfa1" from_work_dir="output.hic.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C primary contig graph"> 360 <data name="hic_pcontig_graph" format="gfa1" from_work_dir="output.hic.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C primary contig graph">
350 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 361 <filter>mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
351 </data> 362 </data>
352 <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph"> 363 <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph">
353 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 364 <filter>mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
354 </data> 365 </data>
355 <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1"> 366 <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
356 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 367 <filter>mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
357 </data> 368 </data>
358 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2"> 369 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
359 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 370 <filter>mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
360 </data> 371 </data>
361 <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig"> 372 <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig">
362 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter> 373 <filter>mode['mode_selector'] != 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
363 </data> 374 </data>
364 <!--Trio outputs with Hi-c reads--> 375 <!--Trio outputs with Hi-c reads-->
365 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw unitig graph"> 376 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw unitig graph">
366 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter> 377 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
367 </data> 378 </data>
434 <assert_contents> 445 <assert_contents>
435 <has_text_matching expression="^S"/> 446 <has_text_matching expression="^S"/>
436 <has_size value="83914" delta="500"/> 447 <has_size value="83914" delta="500"/>
437 </assert_contents> 448 </assert_contents>
438 </output> 449 </output>
439 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" > 450 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1">
440 <assert_contents> 451 <assert_contents>
441 <has_text_matching expression="^S"/> 452 <has_text_matching expression="^S"/>
442 <has_size value="83914" delta="500"/> 453 <has_size value="83914" delta="500"/>
443 </assert_contents> 454 </assert_contents>
444 </output> 455 </output>
445 <output name="hic_raw_initig" ftype="gfa1" > 456 <output name="hic_raw_initig" ftype="gfa1">
446 <assert_contents> 457 <assert_contents>
447 <has_text_matching expression="^S"/> 458 <has_text_matching expression="^S"/>
448 <has_size value="83904" delta="500"/> 459 <has_size value="83904" delta="500"/>
449 </assert_contents> 460 </assert_contents>
450 </output> 461 </output>
604 <assert_contents> 615 <assert_contents>
605 <has_text text="flagged 100 reads, out of 100 lines in file"/> 616 <has_text text="flagged 100 reads, out of 100 lines in file"/>
606 </assert_contents> 617 </assert_contents>
607 </output> 618 </output>
608 </test> 619 </test>
620 <!-- TEST 16: ONT mode -->
621 <test expect_num_outputs="5">
622 <param name="reads" location="https://zenodo.org/records/15075976/files/ont.fastq.gz" ftype="fasta.gz"/>
623 <param name="filter_bits" value="0"/>
624 <param name="mode_selector" value="ont"/>
625 <output name="raw_unitigs" file="hifiasm-out1-ont-raw.gfa" ftype="gfa1"/>
626 <output name="processed_unitigs" file="hifiasm-out1-ont-processed.gfa" ftype="gfa1"/>
627 <output name="primary_contig_graph" file="hifiasm-out1-ont-primary.gfa" ftype="gfa1"/>
628 </test>
609 </tests> 629 </tests>
610 <help><![CDATA[ 630 <help><![CDATA[
611 .. class:: infomark 631 .. class:: infomark
612 632
613 **HiFiASM - a fast de novo assembler** 633 **HiFiASM - a fast de novo assembler**
620 .. class:: infomark 640 .. class:: infomark
621 641
622 **Assembly mode** 642 **Assembly mode**
623 643
624 - *Standard*: Standard assembly can be run in pseudohaplotype mode, or with Hi-C phasing using Hi-C reads from the same individual. 644 - *Standard*: Standard assembly can be run in pseudohaplotype mode, or with Hi-C phasing using Hi-C reads from the same individual.
645 - *ONT*: Enables direct, haplotype-resolved assembly of Oxford Nanopore simplex R10 reads with integrated error correction, optimizing for contiguity without requiring pre-corrected input.
625 - *Trio*: When parental short reads are available, hifiasm can generate a pair of haplotype-resolved assemblies with trio binning. 646 - *Trio*: When parental short reads are available, hifiasm can generate a pair of haplotype-resolved assemblies with trio binning.
626 647
627 ---- 648 ----
628 649
629 .. class:: infomark 650 .. class:: infomark