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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
author bgruening
date Sat, 29 Jan 2022 12:49:28 +0000
parents e100f3f4d80e
children
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1 <tool id="wtdbg" name="WTDBG2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="GPL-3.0-only">
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2 <description>Fast de novo sequence assembler for long noisy reads</description>
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3 <xrefs>
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4 <xref type='bio.tools'>wtdbg2</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">wtdbg</requirement>
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11 </requirements>
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12 <version_command>wtdbg2 -V</version_command>
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13 <command detect_errors="exit_code"><![CDATA[
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14 ## helper function to sort fastqs before fastas in input readsets
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15 #def sort_fastq_fasta(files):
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16 #set fastqs = [f for f in $files if f.is_of_type('fastq')]
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17 #set fastas = [f for f in $files if f.is_of_type('fasta')]
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18 #set out = $fastqs + $fastas
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19 #return $out
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20 #end def
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21
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22 ## prepare readset inputs (must be fastqs then fastas if multiple files)
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23 #set input_reads_sorted = $sort_fastq_fasta($input_reads)
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24
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25 ## perform assembly
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26 wtdbg2
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27 -t \${GALAXY_SLOTS:-4}
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28 -x '${sequencing_technology}'
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29 -g '${genome_size}'
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30 @ASM_OPTIONS@
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31
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32 #for $readset in $input_reads_sorted:
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33 -i '${readset}'
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34 #end for
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35 -fo out
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36
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37 &&
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38 wtpoa-cns
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39 -t \${GALAXY_SLOTS:-4}
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40 -i out.ctg.lay.gz
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41 -fo out.fa
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42 @CNS_OPTIONS@
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43 ]]></command>
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44 <inputs>
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45 <param name="input_reads" type="data" format="fastq,fasta" multiple='true' label="Select input reads from history" help="Select one or more input fastq or fasta files from your history. To select multiple files, use ctrl + click" />
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46 <param name="sequencing_technology" type="select" label="Sequencing Technology" help="Sequencing technology used to generate reads">
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47 <option value="ont">Oxford Nanopore (ont)</option>
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48 <option value="ccs">PacBio CCS (ccs)</option>
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49 <option value="rs">PacBio RSII (rs)</option>
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50 <option value="sq">PacBio Sequel (sq)</option>
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51 </param>
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52 <param name="genome_size" type="text" value="" label="Genome size" help="Estimated genome size. k/m/g suffix is allowed - eg a 4500000bp ecoli genome can be written as 4.5m. For a human genome, use 3.2g">
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53 <sanitizer invalid_char="">
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54 <valid initial="string.letters,string.digits">
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55 <add value="." />
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56 </valid>
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57 </sanitizer>
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58 </param>
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59
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60 <section name="asm" title="Assembly Options" expanded="false">
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61 <param argument="-X" type="float" value="50" label="Read depth" help="(-X) [float] Choose the best [float] depth from input reads. ie if the estimated genome size is 5m, setting this value to 50.0 would select the best 2.5mb worth of reads." />
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62 <param argument="-L" type="integer" value="0" label="Min read length" help="(-L) [int] Choose the longest subread and drop reads shorter than [int]" />
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63 <param argument="-k" type="integer" value="0" min="0" max="23" label="Kmer size" help="(-k) [int] Kmer size, 0 &#8804; k &#8804; 23" />
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64 <param argument="-p" type="integer" value="21" label="Homopolymer-compressed kmer size" help="(-p) [int] Homopolymer-compressed kmer size, 0 &#8804; p &#8804; 23" />
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65 <param argument="-K" type="float" value="1000" label="Max kmer frequency" help="(-K) [float] Filter high frequency kmers where frequency > [float]" />
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66 <param argument="-s" type="float" value="0.05" label="Min read similarity" help="(-s) [float] Min similarity between reads to label as related, calculated by kmer matched length / aligned length" />
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67 <param argument="-e" type="integer" value="3" label="Min edge depth" help="(-e) [int] Min read depth of a valid edge" />
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68 <param name="realign" type="boolean" truevalue="-R" falsevalue="" label="Realignment" help="(-R) Enable realignment mode" />
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69 <param name="contained_reads" type="boolean" truevalue="-A" falsevalue="" label="Contained reads" help="(-A) Keep contained reads during alignment" />
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70 </section>
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71
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72 <section name="cns" title="Consensus Options" expanded="false">
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73 <param argument="-j" type="integer" value="1500" label="Expected length of node" />
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74 <param argument="-M" type="integer" value="2" label="Match score" />
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75 <param argument="-X" type="integer" value="-5" label="Mismatch score" />
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76 <param argument="-I" type="integer" value="-2" label="Insertion score" />
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77 <param argument="-D" type="integer" value="-4" label="Deletion score" />
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78 <param argument="-b" type="integer" value="0" label="Tri-base match bonus" />
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79 <param argument="-H" type="integer" value="-3" label="Homopolymer merge score used in dp-call-cns mode" />
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80 <param argument="-B" type="text" value="64,1024,0.92" label="POA Bandwidth (Wmin,Wmax,mat_rate)" help="mat_rate = matched_bases/total_bases" />
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81 <param argument="-W" type="integer" value="200" label="Window size in the middle of the first read for fast align remaining reads. If -W is negative, will disable fast align, but use the abs(-W) as Band align score cutoff" />
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82 <param argument="-w" type="integer" value="100" label="Min size of aligned size in window. Will default to -W * 0.5" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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83 <param argument="-A" type="boolean" truevalue="-A" falsevalue="" label="Abort TriPOA" help="Abort TriPOA when any read cannot be fast aligned, then try POA" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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84 <param argument="-S" type="select" label="Shuffle mode">
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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85 <option value="0">don't shuffle reads</option>
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86 <option value="1" selected="true">shuffle using shared kmers</option>
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87 <option value="2" >shuffle using subsampling</option>
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88 </param>
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89 <param argument="-R" type="integer" value="16" label="Realignment bandwidth" help="set to 0 to disable" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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90 <param argument="-c" type="select" label="Consensus mode">
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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91 <option value="0" selected="true">run-length</option>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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92 <option value="1">dp-call-cns</option>
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93 </param>
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94 <param argument="-C" type="integer" value="3" label="Min count of bases to call a consensus base" />
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95 <param argument="-F" type="float" value="0.5" label="Min frequency of non-gap bases to call a consensus base" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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96 <param argument="-N" type="integer" value="20" label="Max number of reads in PO-MSA" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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97 </section>
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98 </inputs>
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99 <outputs>
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100 <data name='out_assembly' format='fasta' label="${tool.name} on ${on_string}: assembled contigs" from_work_dir="out.fa" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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101 </outputs>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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102 <tests>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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103 <test expect_num_outputs="1">
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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104 <param name="input_reads" value="test1.fastq" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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105 <param name="sequencing_technology" value="ont" />
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106 <param name="genome_size" value="60k" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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107 <output name="out_assembly">
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108 <assert_contents>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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109 <has_text text=">ctg1 " />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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110 <has_text text=">ctg2 " />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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111 <has_text text=">ctg3 " />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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112 <has_size value="70000" delta="10000" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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113 </assert_contents>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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114 </output>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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115 </test>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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116 <test expect_num_outputs="1">
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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117 <param name="input_reads" value="test1_head.fa,test1_tail.fastq" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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118 <param name="sequencing_technology" value="ont" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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119 <param name="genome_size" value="60k" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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120 <output name="out_assembly">
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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121 <assert_contents>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
bgruening
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122 <has_text text=">ctg1 " />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
bgruening
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123 <has_text text=">ctg2 " />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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124 <has_text text=">ctg3 " />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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125 <has_size value="70000" delta="10000" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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126 </assert_contents>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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127 </output>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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128 </test>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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129 <test expect_num_outputs="1">
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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130 <param name="input_reads" value="test1.fastq" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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131 <param name="sequencing_technology" value="ont" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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132 <param name="genome_size" value="60k" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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133 <section name="asm">
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134 <param name='X' value="10.0" />
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135 <param name='L' value="2000" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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136 <param name='k' value="15" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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137 <param name='p' value="0" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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138 <param name='K' value="500" />
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139 <param name='l' value="1024" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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140 <param name='m' value="200" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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141 <param name='s' value="0.1" />
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142 <param name='e' value="5" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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143 </section>
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144 <output name="out_assembly">
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145 <assert_contents>
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146 <has_text text=">ctg1 " />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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147 <has_text text=">ctg2 " />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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148 <has_text text=">ctg3 " />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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149 <has_size value="50000" delta="10000" />
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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150 </assert_contents>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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151 </output>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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152 </test>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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153 </tests>
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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154 <help><![CDATA[
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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155
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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156 **Wtdbg2**
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157
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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158 |
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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159
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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160 **What it does**
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161
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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162 WTDBG is a de novo assembler for long noisy sequences, based on fuzzy Bruijn graphs (FBG).
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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163
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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164 "Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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165
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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166 **Alignment**
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167
2668027a533b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg commit 05f8373310ce1728426b89f33b643406e0cba54b"
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168 KBM (Kmer-BIN-Mapping) groups k-mers from each non-overlapped sliding 256 bp fragments in long reads into bins.
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169 Bins of which most k-mers are high frequency, are filtered as highly repetitive ones.
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170 Then, KBM searches synteny of matched bin pairs in sequences in a dynamic programming way.
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171 A matched bin pair in two sequences is defined as two bins different by original but share a set of k-mers.
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172 The result of alignments in KBM have the same features of traditional sequence alignment, excepting the unit of
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173 KBM alignments is 256 bp bin instead of single base.
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174
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175 **Assembly**
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176
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177 FBG (Fuzzy Bruijn Graph) is composed of vertices in length of 1024 bp from reads, and edges connecting vertices
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178 in their order on read paths. Comparing with DBG, the size of vertices in FBG are much bigger, thus won't be
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179 sensitive to small repeat. To tolerate high sequencing errors, FBG's vertices are found using gapped
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180 sequence alignments from KBM or other aligners, comparing with searching identical k-mers in DBG.
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181
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182 See the github (https://github.com/ruanjue/wtdbg2) and paper (https://doi.org/10.1038/s41592-019-0669-3) for more information.
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183
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184 |
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185
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186 **Input**
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187
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188 One or more fastq or fasta files. Can be in any fastq/fasta format with any valid exension.
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189
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190 |
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191
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192 **Output**
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193
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194 Assembled contigs (the assembled genome).
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195 To polish, use external tools such as pilon, racon, medaka, nextpolish etc.
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196
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197 |
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198
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199 **Sequencing Technology Preset Information**
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200
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201 - Oxford Nanopore (ont) (genome size < 1G): -p 0 -k 15 -AS 2 -s 0.05 -L 5000
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202 - Oxford Nanopore (ont) (genome size >= 1G): -p 19 -AS 2 -s 0.05 -L 5000
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203 - PacBio CCS (ccs): -p 21 -k 0 -AS 4 -K 0.05 -s 0.5
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204 - PacBio RSII (rs): -p 21 -S 4 -s 0.05 -L 5000
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205 - PacBio Sequel (sq) (genome size < 1G): -p 0 -k 15 -AS 2 -s 0.05 -L 5000
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206 - PacBio Sequel (sq) (genome size >= 1G): -p 19 -AS 2 -s 0.05 -L 5000
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207
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208 |
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209 ]]></help>
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210 <expand macro="citations" />
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211 </tool>