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comparison hifiasm.xml @ 16:41cea2aa2dce draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
author bgruening
date Fri, 20 Oct 2023 22:03:32 +0000
parents 60024a528cbd
children 0ee0c3089254
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15:60024a528cbd 16:41cea2aa2dce
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@">0.19.7</token> 4 <token name="@TOOL_VERSION@">0.19.7</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</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>
10 </macros> 10 </macros>
48 ln -s '$read' $inputfile && 48 ln -s '$read' $inputfile &&
49 $ultralong_inputs.append($inputfile) 49 $ultralong_inputs.append($inputfile)
50 #end for 50 #end for
51 #end if 51 #end if
52 #if str($mode.mode_selector) == 'trio': 52 #if str($mode.mode_selector) == 'trio':
53 #for idx, read in enumerate($mode.hap1_reads): 53 #if str($mode.trioinput.trio_input_selector) == 'reads':
54 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension) 54 #for idx, read in enumerate($mode.trioinput.hap1_reads):
55 ln -s '$read' $inputfile && 55 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
56 $hap1_inputs.append($inputfile) 56 ln -s '$read' $inputfile &&
57 #end for 57 $hap1_inputs.append($inputfile)
58 #for idx, read in enumerate($mode.hap2_reads): 58 #end for
59 #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension) 59 #for idx, read in enumerate($mode.trioinput.hap2_reads):
60 ln -s '$read' $inputfile && 60 #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
61 $hap2_inputs.append($inputfile) 61 ln -s '$read' $inputfile &&
62 #end for 62 $hap2_inputs.append($inputfile)
63 #set $hap1_filenames = ' '.join($hap1_inputs) 63 #end for
64 #set $hap2_filenames = ' '.join($hap2_inputs) 64 #set $hap1_filenames = ' '.join($hap1_inputs)
65 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames && 65 #set $hap2_filenames = ' '.join($hap2_inputs)
66 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames && 66 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
67 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
68 #end if
69 #if str($mode.trioinput.trio_input_selector) == 'lists':
70 #set $hap1_filenames = $mode.trioinput.hap1_list
71 #set $hap2_filenames = $mode.trioinput.hap2_list
72 #end if
67 #end if 73 #end if
68 hifiasm 74 hifiasm
69 -t \${GALAXY_SLOTS:-1} 75 -t \${GALAXY_SLOTS:-1}
70 -o output 76 -o output
71 -f $filter_bits 77 -f $filter_bits
97 #if $assembly_options.hom_cov 103 #if $assembly_options.hom_cov
98 --hom-cov $assembly_options.hom_cov 104 --hom-cov $assembly_options.hom_cov
99 #end if 105 #end if
100 #end if 106 #end if
101 #if str($mode.mode_selector) == 'trio': 107 #if str($mode.mode_selector) == 'trio':
102 -1 hap1.yak 108 #if str($mode.trioinput.trio_input_selector) == 'reads':
103 -2 hap2.yak 109 -1 hap1.yak
110 -2 hap2.yak
111 #end if
112 #if str($mode.trioinput.trio_input_selector) == 'lists':
113 -3 $hap1_filenames
114 -4 $hap2_filenames
115 #end if
104 -c $mode.max_kmers 116 -c $mode.max_kmers
105 -d $mode.min_kmers 117 -d $mode.min_kmers
118 $mode.trio_dual
106 #end if 119 #end if
107 #if str($purge_options.purge_selector) == 'set': 120 #if str($purge_options.purge_selector) == 'set':
108 -l $purge_options.purge_level 121 -l $purge_options.purge_level
109 -s $purge_options.similarity_threshold 122 -s $purge_options.similarity_threshold
110 -O $purge_options.minimum_overlap 123 -O $purge_options.minimum_overlap
173 <when value="standard"> 186 <when value="standard">
174 <expand macro="reads" /> 187 <expand macro="reads" />
175 </when> 188 </when>
176 <when value="trio"> 189 <when value="trio">
177 <expand macro="reads" /> 190 <expand macro="reads" />
178 <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" /> 191 <conditional name="trioinput">
179 <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" /> 192 <param name="trio_input_selector" type="select" label="What parental information are you using?">
193 <option value="reads">Parental reads (FASTQ files, gzipped or otherwise)</option>
194 <option value="lists">Lists of reads assigned by parent (text files)</option>
195 </param>
196 <when value="reads">
197 <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />
198 <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />
199 </when>
200 <when value="lists">
201 <param name="hap1_list" type="data" format="txt,tabular" label="Haplotype 1 read list" />
202 <param name="hap2_list" type="data" format="txt,tabular" label="Haplotype 2 read list" />
203 </when>
204 </conditional>
180 <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" /> 205 <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" />
181 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" /> 206 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
182 <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" /> 207 <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />
208 <param name="trio_dual" argument="--trio-dual" type="boolean" truevalue="--trio-dual" falsevalue="" label="Utilize homology information to correct trio-phasing errors" />
183 </when> 209 </when>
184 </conditional> 210 </conditional>
185 <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter" /> 211 <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter" />
186 <conditional name="assembly_options"> 212 <conditional name="assembly_options">
187 <param name="assembly_selector" type="select" label="Assembly options"> 213 <param name="assembly_selector" type="select" label="Assembly options">
426 <!-- TEST 5: Test trio mode --> 452 <!-- TEST 5: Test trio mode -->
427 <test expect_num_outputs="5"> 453 <test expect_num_outputs="5">
428 <param name="filter_bits" value="0"/> 454 <param name="filter_bits" value="0"/>
429 <conditional name="mode"> 455 <conditional name="mode">
430 <param name="mode_selector" value="trio"/> 456 <param name="mode_selector" value="trio"/>
431 <param name="reads" value="child.fasta.gz"/> 457 <param name="trio_input_selector" value="reads"/>
432 <param name="hap1_reads" value="paternal.fasta.gz"/> 458 <conditional name="trioinput">
433 <param name="hap2_reads" value="maternal.fasta.gz"/> 459 <param name="reads" value="child.fasta.gz"/>
460 <param name="hap1_reads" value="paternal.fasta.gz"/>
461 <param name="hap2_reads" value="maternal.fasta.gz"/>
462 </conditional>
434 <param name="max_kmers" value="2"/> 463 <param name="max_kmers" value="2"/>
435 <param name="min_kmers" value="5"/> 464 <param name="min_kmers" value="5"/>
436 </conditional> 465 </conditional>
437 <assert_command> 466 <assert_command>
438 <has_text text="-1 hap1.yak" /> 467 <has_text text="-1 hap1.yak" />
554 <param name="filter_bits" value="0" /> 583 <param name="filter_bits" value="0" />
555 <param name="mode_selector" value="standard" /> 584 <param name="mode_selector" value="standard" />
556 <param name="bins_out" value="yes" /> 585 <param name="bins_out" value="yes" />
557 <output_collection name="bin_files" type="list" count="3" /> 586 <output_collection name="bin_files" type="list" count="3" />
558 </test> 587 </test>
588 <!-- TEST 15: Test trio LIST mode -->
589 <test expect_num_outputs="6">
590 <param name="filter_bits" value="0"/>
591 <param name="log_out" value="yes"/>
592 <conditional name="mode">
593 <param name="mode_selector" value="trio"/>
594 <param name="reads" value="child.fasta.gz"/>
595 <conditional name="trioinput">
596 <param name="trio_input_selector" value="lists"/>
597 <param name="hap1_list" value="maternal.headers.txt"/>
598 <param name="hap2_list" value="paternal.headers.txt"/>
599 </conditional>
600 <param name="max_kmers" value="2"/>
601 <param name="min_kmers" value="5"/>
602 </conditional>
603 <output name="log_file" ftype="txt">
604 <assert_contents>
605 <has_text text="flagged 100 reads, out of 100 lines in file"/>
606 </assert_contents>
607 </output>
608 </test>
559 </tests> 609 </tests>
560 <help><![CDATA[ 610 <help><![CDATA[
561 .. class:: infomark 611 .. class:: infomark
562 612
563 **HiFiASM - a fast de novo assembler** 613 **HiFiASM - a fast de novo assembler**