Mercurial > repos > bgruening > hifiasm
comparison hifiasm.xml @ 4:3f7be05a1597 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
author | bgruening |
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date | Wed, 22 Sep 2021 21:13:59 +0000 |
parents | 9ef6920c3089 |
children | 045c7c3d8e59 |
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3:9ef6920c3089 | 4:3f7be05a1597 |
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1 <tool id="hifiasm" name="Hifiasm" version="@VERSION@+galaxy0"> | 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="@VERSION@">0.15.4</token> | 4 <token name="@TOOL_VERSION@">0.16.1</token> |
5 <token name="@VERSION_SUFFIX@">0</token> | |
5 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> | 6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> |
6 <xml name="reads"> | 7 <xml name="reads"> |
7 <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" /> |
8 </xml> | 9 </xml> |
9 </macros> | 10 </macros> |
10 <requirements> | 11 <requirements> |
11 <requirement type="package" version="@VERSION@">hifiasm</requirement> | 12 <requirement type="package" version="@TOOL_VERSION@">hifiasm</requirement> |
12 <requirement type="package" version="0.1">yak</requirement> | 13 <requirement type="package" version="0.1">yak</requirement> |
13 </requirements> | 14 </requirements> |
14 <version_command>hifiasm --version</version_command> | 15 <version_command>hifiasm --version</version_command> |
15 <command detect_errors="exit_code"> | 16 <command detect_errors="exit_code"> |
16 | 17 |
51 -N $advanced_options.max_overlaps | 52 -N $advanced_options.max_overlaps |
52 -r $advanced_options.correction_rounds | 53 -r $advanced_options.correction_rounds |
53 #if $advanced_options.min_hist_cnt: | 54 #if $advanced_options.min_hist_cnt: |
54 --min-hist-cnt $advanced_options.min_hist_cnt | 55 --min-hist-cnt $advanced_options.min_hist_cnt |
55 #end if | 56 #end if |
57 --max-kocc $advanced_options.max_kocc | |
58 #if $advanced_options.hg_size | |
59 --hg-size $advanced_options.hg_size | |
60 #end if | |
61 | |
56 #end if | 62 #end if |
57 #if str($assembly_options.assembly_selector) == 'set': | 63 #if str($assembly_options.assembly_selector) == 'set': |
58 -a $assembly_options.cleaning_rounds | 64 -a $assembly_options.cleaning_rounds |
59 -z $assembly_options.adapter_length | 65 -z $assembly_options.adapter_length |
60 -m $assembly_options.pop_contigs | 66 -m $assembly_options.pop_contigs |
62 -n $assembly_options.remove_tips | 68 -n $assembly_options.remove_tips |
63 -x $assembly_options.max_overlap | 69 -x $assembly_options.max_overlap |
64 -y $assembly_options.min_overlap | 70 -y $assembly_options.min_overlap |
65 $assembly_options.disable_post_join | 71 $assembly_options.disable_post_join |
66 $assembly_options.ignore_error_corrected | 72 $assembly_options.ignore_error_corrected |
73 #if $assembly_options.hom_cov | |
74 --hom-cov $assembly_options.hom_cov | |
75 #end if | |
67 #end if | 76 #end if |
68 #if str($mode.mode_selector) == 'trio': | 77 #if str($mode.mode_selector) == 'trio': |
69 -1 hap1.yak | 78 -1 hap1.yak |
70 -2 hap2.yak | 79 -2 hap2.yak |
71 -c $mode.max_kmers | 80 -c $mode.max_kmers |
73 #end if | 82 #end if |
74 #if str($purge_options.purge_selector) == 'set': | 83 #if str($purge_options.purge_selector) == 'set': |
75 -l $purge_options.purge_level | 84 -l $purge_options.purge_level |
76 -s $purge_options.similarity_threshold | 85 -s $purge_options.similarity_threshold |
77 -O $purge_options.minimum_overlap | 86 -O $purge_options.minimum_overlap |
78 #if $purge_options.purge_cov: | 87 #if $purge_options.purge_max: |
79 --purge-cov $purge_options.purge_cov | 88 --purge-max $purge_options.purge_max |
80 #end if | 89 #end if |
81 #if $purge_options.n_hap: | 90 #if $purge_options.n_hap: |
82 --n-hap $purge_options.n_hap | 91 --n-hap $purge_options.n_hap |
83 #end if | 92 #end if |
84 #end if | 93 #end if |
133 <option value="blank">Leave default</option> | 142 <option value="blank">Leave default</option> |
134 <option value="set">Specify</option> | 143 <option value="set">Specify</option> |
135 </param> | 144 </param> |
136 <when value="blank" /> | 145 <when value="blank" /> |
137 <when value="set"> | 146 <when value="set"> |
138 <param name="hifiasm_kmer_length" argument="-k" type="integer" min="0" max="64" value="51" label="HiFiasm k-mer length" /> | 147 <param name="hifiasm_kmer_length" argument="-k" type="integer" min="0" max="64" value="51" label="Hifiasm k-mer length" /> |
139 <param name="window_size" argument="-w" type="integer" min="0" value="51" label="Minimizer window size" /> | 148 <param name="window_size" argument="-w" type="integer" min="0" value="51" label="Minimizer window size" /> |
140 <param name="drop_kmers" argument="-D" type="float" value="5.0" label="Drop k-mers" help="K-mers that occur more than this value multiplied by the coverage will be discarded" /> | 149 <param name="drop_kmers" argument="-D" type="float" value="5.0" label="Drop k-mers" help="K-mers that occur more than this value multiplied by the coverage will be discarded" /> |
141 <param name="max_overlaps" argument="-N" type="integer" value="100" label="Maximum overlaps to consider" help="The software selects the larger of this value and the k-mer count multiplied by coverage" /> | 150 <param name="max_overlaps" argument="-N" type="integer" value="100" label="Maximum overlaps to consider" help="The software selects the larger of this value and the k-mer count multiplied by coverage" /> |
142 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" /> | 151 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" /> |
143 <param argument="--min-hist-cnt" type="integer" min="0" value="" optional="true" label="Minimum count threshold" help="When analyzing the k-mer spectrum, ignore counts below this value" /> | 152 <param argument="--min-hist-cnt" type="integer" min="0" value="" optional="true" label="Minimum count threshold" help="When analyzing the k-mer spectrum, ignore counts below this value" /> |
153 <param argument="--max-kocc" type="integer" min="0" value="20000" label="Maximum k-mer ocurrence" help="Employ k-mers occurring less than INT times to rescue repetitive overlaps" /> | |
154 <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size" help="Estimated haploid genome size used for inferring read coverage. If not provided, this parameter will be infered by hifism. Common suffices are required, for example, 100m or 3g"> | |
155 <sanitizer invalid_char=""> | |
156 <valid initial="string.digits"> | |
157 <add value="k" /> | |
158 <add value="K" /> | |
159 <add value="m" /> | |
160 <add value="M" /> | |
161 <add value="G" /> | |
162 <add value="g" /> | |
163 </valid> | |
164 </sanitizer> | |
165 <validator type="regex">[0-9kKmMGg]+</validator> | |
166 </param> | |
144 </when> | 167 </when> |
145 </conditional> | 168 </conditional> |
146 | 169 |
147 <conditional name="assembly_options"> | 170 <conditional name="assembly_options"> |
148 <param name="assembly_selector" type="select" label="Assembly options"> | 171 <param name="assembly_selector" type="select" label="Assembly options"> |
158 <param name="remove_tips" argument="-n" type="integer" value="3" label="Tip unitigs" help="Keep only tip unitigs with a number of reads greater than or equal to this value" /> | 181 <param name="remove_tips" argument="-n" type="integer" value="3" label="Tip unitigs" help="Keep only tip unitigs with a number of reads greater than or equal to this value" /> |
159 <param name="max_overlap" argument="-x" type="float" min="0" max="1" value="0.8" label="Maximum overlap drop ratio" help="This option is used with -r. Given a node N in the assembly graph, let max(N) be the length of the largest overlap of N. Hifiasm iteratively drops overlaps of N if their length/max(N) are below a threshold controlled by -x. Hifiasm applies -r rounds of short overlap removal with an increasing threshold between -x and -y"/> | 182 <param name="max_overlap" argument="-x" type="float" min="0" max="1" value="0.8" label="Maximum overlap drop ratio" help="This option is used with -r. Given a node N in the assembly graph, let max(N) be the length of the largest overlap of N. Hifiasm iteratively drops overlaps of N if their length/max(N) are below a threshold controlled by -x. Hifiasm applies -r rounds of short overlap removal with an increasing threshold between -x and -y"/> |
160 <param name="min_overlap" argument="-y" type="float" min="0" max="1" value="0.2" label="Minimum overlap drop ratio" help="This option is used with -r. Given a node N in the assembly graph, let max(N) be the length of the largest overlap of N. Hifiasm iteratively drops overlaps of N if their length/max(N) are over a threshold controlled by -y. Hifiasm applies -r rounds of short overlap removal with an increasing threshold between -x and -y"/> | 183 <param name="min_overlap" argument="-y" type="float" min="0" max="1" value="0.2" label="Minimum overlap drop ratio" help="This option is used with -r. Given a node N in the assembly graph, let max(N) be the length of the largest overlap of N. Hifiasm iteratively drops overlaps of N if their length/max(N) are over a threshold controlled by -y. Hifiasm applies -r rounds of short overlap removal with an increasing threshold between -x and -y"/> |
161 <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" /> | 184 <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" /> |
162 <param name="ignore_error_corrected" argument="-i" type="boolean" truevalue="-i" falsevalue="" value="False" label="Ignore error corrected reads and overlaps" help="Ignore error corrected reads and overlaps saved in prefix.*.bin files. Apart from assembly graphs, hifiasm also outputs three binary files that save alloverlap information during assembly step. With these files, hifiasm can avoid the time-consuming all-to-all overlap calculation step, and do the assembly directly and quickly. This might be helpful when users want to get an optimized assembly by multiple rounds of experiments with different parameters." /> | 185 <param name="ignore_error_corrected" argument="-i" type="boolean" truevalue="-i" falsevalue="" value="False" label="Ignore error corrected reads and overlaps" help="Ignore error corrected reads and overlaps saved in prefix.*.bin files. Apart from assembly graphs, hifiasm also outputs three binary files that save alloverlap information during assembly step. With these files, hifiasm can avoid the time-consuming all-to-all overlap calculation step, and do the assembly directly and quickly. This might be helpful when users want to get an optimized assembly by multiple rounds of experiments with different parameters." /> |
186 <param argument="--hom-cov" type="integer" optional="True" value="" label="Homozygous read coverage" /> | |
163 </when> | 187 </when> |
164 </conditional> | 188 </conditional> |
165 | 189 |
166 <conditional name="purge_options"> | 190 <conditional name="purge_options"> |
167 <param name="purge_selector" type="select" label="Options for purging duplicates"> | 191 <param name="purge_selector" type="select" label="Options for purging duplicates"> |
176 <option value="2">Aggressive (2)</option> | 200 <option value="2">Aggressive (2)</option> |
177 <option value="3">Aggressive - high heterozygosity rate (3)</option> | 201 <option value="3">Aggressive - high heterozygosity rate (3)</option> |
178 </param> | 202 </param> |
179 <param name="similarity_threshold" argument="-s" type="float" min="0" max="1" value="0.75" label="Similarity threshold for duplicate haplotigs" /> | 203 <param name="similarity_threshold" argument="-s" type="float" min="0" max="1" value="0.75" label="Similarity threshold for duplicate haplotigs" /> |
180 <param name="minimum_overlap" argument="-O" type="integer" value="1" label="Minimum overlapped reads for duplicate haplotigs" /> | 204 <param name="minimum_overlap" argument="-O" type="integer" value="1" label="Minimum overlapped reads for duplicate haplotigs" /> |
181 <param argument="--purge-cov" type="integer" optional="true" label="Coverage upper bound" help="If not set, this will be determined automatically" /> | 205 <param argument="--purge-max" type="integer" optional="true" label="Coverage upper bound" help="If not set, this will be determined automatically" /> |
182 <param argument="--n-hap" type="integer" min="0" value="" optional="True" label="Assumtion of haplotype number" help="A haplotype is defined as the combination of alleles for different polymorphisms that occur on the same chromosome." /> | 206 <param argument="--n-hap" type="integer" min="0" value="" optional="true" label="Assumtion of haplotype number" help="A haplotype is defined as the combination of alleles for different polymorphisms that occur on the same chromosome." /> |
183 </when> | 207 </when> |
184 </conditional> | 208 </conditional> |
185 | 209 |
186 <conditional name="hic_partition"> | 210 <conditional name="hic_partition"> |
187 <param name="hic_partition_selector" type="select" label="Options for Hi-C-partition"> | 211 <param name="hic_partition_selector" type="select" label="Options for Hi-C-partition"> |
384 <assert_contents> | 408 <assert_contents> |
385 <has_size value="0"/> | 409 <has_size value="0"/> |
386 </assert_contents> | 410 </assert_contents> |
387 </output> | 411 </output> |
388 </test> | 412 </test> |
413 <!-- Test max_kooc option --> | |
414 <test> | |
415 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | |
416 <param name="filter_bits" value="0" /> | |
417 <param name="mode_selector" value="standard" /> | |
418 <conditional name="advanced_options"> | |
419 <param name="advanced_selector" value="set"/> | |
420 <param name="max_kooc" value="21000"/> | |
421 </conditional> | |
422 <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" /> | |
423 <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" /> | |
424 <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" /> | |
425 <output name="alternate_contig_graph" ftype="gfa1"> | |
426 <assert_contents> | |
427 <has_size value="0"/> | |
428 </assert_contents> | |
429 </output> | |
430 </test> | |
431 <!-- Test hg-size option --> | |
432 <test> | |
433 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | |
434 <param name="filter_bits" value="0" /> | |
435 <param name="mode_selector" value="standard" /> | |
436 <conditional name="advanced_options"> | |
437 <param name="advanced_selector" value="set"/> | |
438 <param name="hg_size" value="1k"/> | |
439 </conditional> | |
440 <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" /> | |
441 <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" /> | |
442 <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" /> | |
443 <output name="alternate_contig_graph" ftype="gfa1"> | |
444 <assert_contents> | |
445 <has_size value="0"/> | |
446 </assert_contents> | |
447 </output> | |
448 </test> | |
449 <!-- Test ignore-error-corrected option --> | |
450 <test> | |
451 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" /> | |
452 <param name="filter_bits" value="0" /> | |
453 <param name="mode_selector" value="standard" /> | |
454 <conditional name="assembly_options"> | |
455 <param name="assembly_selector" value="set"/> | |
456 <param name="hom-cov" value="1000"/> | |
457 </conditional> | |
458 <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" /> | |
459 <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" /> | |
460 <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" /> | |
461 <output name="alternate_contig_graph" ftype="gfa1"> | |
462 <assert_contents> | |
463 <has_size value="0"/> | |
464 </assert_contents> | |
465 </output> | |
466 </test> | |
389 </tests> | 467 </tests> |
390 <help><![CDATA[ | 468 <help><![CDATA[ |
391 *********************************** | 469 *********************************** |
392 HiFiASM - a fast de novo assembler | 470 HiFiASM - a fast de novo assembler |
393 *********************************** | 471 *********************************** |