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annotate hifiasm.xml @ 0:bf0a4667e3ce draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
author bgruening
date Tue, 02 Mar 2021 20:23:49 +0000
parents
children 6505bd37670d
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bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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1 <tool id="hifiasm" name="Hifiasm" version="@VERSION@">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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2 <description>de novo assembler</description>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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3 <macros>
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4 <token name="@VERSION@">0.14</token>
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5 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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6 <xml name="reads">
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7 <param name="reads" type="data" format="@FORMATS@" label="Input reads" />
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8 </xml>
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9 </macros>
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10 <requirements>
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11 <requirement type="package" version="@VERSION@">hifiasm</requirement>
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12 <requirement type="package" version="0.1">yak</requirement>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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13 </requirements>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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14 <version_command>hifiasm --version</version_command>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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15 <command detect_errors="exit_code">
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16 <![CDATA[
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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17 #if str($mode.mode_selector) == 'standard':
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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18 ln -s '$mode.reads' input.${mode.reads.extension} &&
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19 #else:
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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20 ln -s '$mode.hap1_reads' hap1_reads.${mode.hap1_reads.extension} &&
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21 ln -s '$mode.hap2_reads' hap2_reads.${mode.hap2_reads.extension} &&
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22 yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap1.yak hap1_reads.${mode.hap1_reads.extension} &&
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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23 yak count -k31 -b37 -t\${GALAXY_SLOTS:-1} -o hap2.yak hap2_reads.${mode.hap2_reads.extension} &&
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24 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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25 hifiasm -i input.${mode.reads.extension} -t \${GALAXY_SLOTS:-1} -o output -f $filter_bits
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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26 #if str($advanced_options.advanced_selector) == 'set':
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27 -z $advanced_options.adapter_length
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28 -k $advanced_options.kmer_length
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29 -w $advanced_options.window_size
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30 -D $advanced_options.drop_kmers
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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31 -N $advanced_options.max_overlaps
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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32 -r $advanced_options.correction_rounds
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33 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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34 #if str($assembly_options.assembly_selector) == 'set':
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35 -a $assembly_options.cleaning_rounds
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36 -m $assembly_options.pop_contigs
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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37 -p $assembly_options.pop_unitigs
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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38 -n $assembly_options.remove_tips
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39 -x $assembly_options.max_overlap
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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40 -y $assembly_options.min_overlap
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41 $assembly_options.disable_post_join
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42 --pb-range $assembly_options.pb_range
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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43 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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44 #if str($mode.mode_selector) == 'trio':
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45 -1 hap1.yak
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46 -2 hap2.yak
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47 -c $mode.max_kmers
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48 -d $mode.min_kmers
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49 #end if
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50 #if str($purge_options.purge_selector) == 'set':
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51 -l $purge_options.purge_level
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52 -s $purge_options.similarity_threshold
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53 -O $purge_options.minimum_overlap
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54 #if $purge_options.purge_cov:
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55 --purge-cov $purge_options.purge_cov
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56 #end if
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57 $purge_options.high_het
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58 #end if
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59 ]]>
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60 </command>
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61 <inputs>
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62 <conditional name="mode">
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63 <param name="mode_selector" type="select" label="Assembly mode">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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64 <option value="standard">Standard</option>
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65 <option value="trio">Trio mode</option>
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66 </param>
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67 <when value="standard">
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68 <expand macro="reads" />
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69 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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70 <when value="trio">
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71 <expand macro="reads" />
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72 <param name="hap1_reads" type="data" format="fastq,fastq.gz" label="Haplotype 1 reads" />
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73 <param name="hap2_reads" type="data" format="fastq,fastq.gz" label="Haplotype 2 reads" />
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74 <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" />
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75 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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76 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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77 </conditional>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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78 <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" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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79 <conditional name="advanced_options">
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80 <param name="advanced_selector" type="select" label="Advanced options">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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81 <option value="blank">Leave default</option>
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82 <option value="set">Specify</option>
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83 </param>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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84 <when value="blank" />
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85 <when value="set">
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86 <param name="adapter_length" argument="-z" type="integer" min="0" value="0" label="Length of adapters to be removed" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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87 <param name="kmer_length" argument="-k" type="integer" min="0" max="64" value="51" label="K-mer length" />
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88 <param name="window_size" argument="-w" type="integer" min="0" value="51" label="Minimizer window size" />
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89 <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" />
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90 <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" />
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91 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" />
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92 </when>
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93 </conditional>
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94 <conditional name="assembly_options">
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95 <param name="assembly_selector" type="select" label="Assembly options">
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96 <option value="blank">Leave default</option>
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97 <option value="set">Specify</option>
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98 </param>
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99 <when value="blank" />
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100 <when value="set">
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101 <param name="cleaning_rounds" argument="-a" type="integer" value="4" label="Cleaning rounds" />
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102 <param name="pop_contigs" argument="-m" type="integer" value="10000000" label="Minimum contig bubble size" help="Pop contig graph bubbles smaller than this value" />
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103 <param name="pop_unitigs" argument="-p" type="integer" value="100000" label="Minimum unitig bubble size" help="Pop unitig graph bubbles smaller than this value" />
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104 <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" />
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105 <param name="max_overlap" argument="-x" type="float" min="0" max="1" value="0.8" label="Maximum overlap drop ratio" />
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106 <param name="min_overlap" argument="-y" type="float" min="0" max="1" value="0.2" label="Minimum overlap drop ratio" />
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107 <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" />
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108 <param argument="--pb-range" type="integer" min="0" max="100" value="0" label="Inconsistent contigs" help="If this option is set to a value greater than zero the tool generates an additional BED dataset containing regions that are &gt;= x% inconsistent." />
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109 </when>
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110 </conditional>
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111 <conditional name="purge_options">
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112 <param name="purge_selector" type="select" label="Options for purging duplicates">
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113 <option value="blank">Leave default</option>
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114 <option value="set">Specify</option>
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115 </param>
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116 <when value="blank" />
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117 <when value="set">
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118 <param name="purge_level" argument="-l" type="select" label="Purge level">
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119 <option value="0" selected="true">None</option>
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120 <option value="1">Light</option>
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121 <option value="2">Aggressive</option>
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122 </param>
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123 <param name="similarity_threshold" argument="-s" type="float" min="0" max="1" value="0.75" label="Similarity threshold for duplicate haplotigs" />
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124 <param name="minimum_overlap" argument="-O" type="integer" value="1" label="Minimum overlapped reads for duplicate haplotigs" />
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125 <param argument="--purge-cov" type="integer" optional="true" label="Coverage upper bound" help="If not set, this will be determined automatically" />
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126 <param argument="--high-het" type="boolean" truevalue="--high-het" falsevalue="" label="Experimental high-heterozygosity mode" help="NB: May be unstable" />
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127 </when>
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128 </conditional>
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129 </inputs>
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130 <outputs>
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131 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string} Haplotype-resolved raw unitig graph">
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132 <filter>mode['mode_selector'] == 'standard'</filter>
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133 </data>
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134 <data name="raw_unitigs" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string} Haplotype-resolved raw unitig graph">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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135 <filter>mode['mode_selector'] == 'trio'</filter>
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136 </data>
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137 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string} Processed unitig graph">
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138 <filter>mode['mode_selector'] == 'standard'</filter>
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139 </data>
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140 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string} Primary assembly contig graph">
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141 <filter>mode['mode_selector'] == 'standard'</filter>
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142 </data>
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143 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string} Alternate assembly contig graph">
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144 <filter>mode['mode_selector'] == 'standard'</filter>
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145 </data>
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146 <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} ${mode.hap1_reads.name} contig graph">
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147 <filter>mode['mode_selector'] == 'trio'</filter>
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148 </data>
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149 <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} ${mode.hap2_reads.name} contig graph">
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150 <filter>mode['mode_selector'] == 'trio'</filter>
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151 </data>
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152 </outputs>
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153 <tests>
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154 <test>
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155 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
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156 <param name="filter_bits" value="0" />
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157 <param name="mode_selector" value="standard" />
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158 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
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159 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
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160 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
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161 <output name="alternate_contig_graph" file="hifiasm-out1-alternate.gfa" ftype="gfa1" />
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162 </test>
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163 </tests>
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164 <help><![CDATA[
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165 ***********************************
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166 HiFiASM - a fast de novo assembler
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167 ***********************************
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168
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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169 Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.
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170
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171 #### Assembly mode
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172 - *Standard*
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173 - *Trio* When parental short reads are available, hifiasm can generate a pair of haplotype-resolved assemblies with trio binning.
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174
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175 #### Trio Options
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176 - *Haplotype 1 reads* : list of hap1/paternal read names
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177 - *Haplotype 2 reads* : list of hap2/maternal read names
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178 - *Lower bound of the binned k-mer's frequency*
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179 - *Upper bound of the binned k-mer's frequency*
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180
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181 *Bits for bloom filter* (-f) - A value of 0 disables the bloom filter for small genomes. For genomes much larger than human, applying -f 38 or even - f39 is preferred to save memory on k-mer counting.
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182
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183 #### Advanced options
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184 - *Length of adapters to be removed* Old HiFi reads may contain short adapter sequences at the ends of reads. You can specify 20 to trim both ends of reads by 20bp.
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185 - *K-mer length* (must be <64)
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186 - *Minimizer window size*
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187 - *Drop K-mers* K-mers that occur more than this value multiplied by the coverage will be discarded
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188 - *Maximum overlaps to consider* consider up to max(-D*coverage,-N) overlaps for each oriented read
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189 - *Correction rounds* round of correction
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190
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191 #### Assembly options
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192 - *Cleaning rounds* round of assembly cleaning
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193 - *Minimum contig bubble* size Pop contig graph bubbles smaller than this value
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194 - *Minimum unitig bubble* size Pop unitig graph bubbles smaller than this value
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195 - *Tip unitigs* Keep only tip unitigs with a number of reads greater than or equal to this value
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196 - *Maximum overlap drop ratio*
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197 - *Minimum overlap drop ratio*
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198 - *Skip post join contigs step* disable post join contigs step which may improve N50
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199 - *Inconsistent contigs* If this option is set to a value greater than zero the tool generates an additional BED dataset containing regions that are &gt;= x% inconsistent.
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200
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201 #### Options for purging duplicates
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202 - *Purge level* 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip]
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203 - *Similarity threshold for duplicate haplotigs*
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204 - *Minimum overlapped reads for duplicate haplotigs*
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205 - *Coverage upper bound* If not set, this will be determined automatically
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206 - *Experimental high-heterozygosity mode* enable this mode for high heterozygosity sample NB: May be unstable
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207
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208
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209 ### Outputs
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210
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211 Non Trio assembly
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212 - Haplotype-resolved raw unitig graph in GFA format. This graph keeps all haplotype information, including somatic mutations and recurrent sequencing errors.
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213 - Haplotype-resolved processed unitig graph without small bubbles : Small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information.
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214 - Primary assembly contig graph : This graph collapses different haplotypes.
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215 - Alternate assembly contig graph : This graph consists of all assemblies that are discarded in primary contig graph.
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216
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217
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218 Trio assembly
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219 - Haplotype-resolved raw unitig graph in GFA format . This graph keeps all haplotype information.
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220 - Phased paternal/haplotype1 contig graph. This graph keeps the phased paternal/haplotype1 assembly.
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221 - Phased maternal/haplotype2 contig graph. This graph keeps the phased maternal/haplotype2 assembly.
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222
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223
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224
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225 ]]></help>
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226 <citations>
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227 <citation type="doi">10.1038/s41592-020-01056-5</citation>
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228 </citations>
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229 </tool>