Mercurial > repos > bgruening > hifiasm

annotate hifiasm.xml @ 4:3f7be05a1597 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
author bgruening
date Wed, 22 Sep 2021 21:13:59 +0000
parents 9ef6920c3089
children 045c7c3d8e59
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rev   line source
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
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1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2
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2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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3 <macros>
4
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4 <token name="@TOOL_VERSION@">0.16.1</token>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
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5 <token name="@VERSION_SUFFIX@">0</token>
0
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6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
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7 <xml name="reads">
1
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8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
0
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9 </xml>
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10 </macros>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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11 <requirements>
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
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12 <requirement type="package" version="@TOOL_VERSION@">hifiasm</requirement>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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13 <requirement type="package" version="0.1">yak</requirement>
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14 </requirements>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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15 <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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16 <command detect_errors="exit_code">
2
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17
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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18 <![CDATA[
1
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19 #set $input_files = list()
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20 #set $hap1_inputs = list()
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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21 #set $hap2_inputs = list()
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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22 #for idx, read in enumerate($mode.reads):
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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23 #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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24 ln -s '$read' $inputfile &&
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25 $input_files.append($inputfile)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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26 #end for
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27 #set $input_filenames = ' '.join($input_files)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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28 #if str($mode.mode_selector) == 'trio':
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
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29 #for idx, read in enumerate($mode.hap1_reads):
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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30 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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31 ln -s '$read' $inputfile &&
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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32 $hap1_inputs.append($inputfile)
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33 #end for
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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34 #for idx, read in enumerate($mode.hap2_reads):
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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35 #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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36 ln -s '$read' $inputfile &&
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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37 $hap2_inputs.append($inputfile)
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38 #end for
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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39 #set $hap1_filenames = ' '.join($hap1_inputs)
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40 #set $hap2_filenames = ' '.join($hap2_inputs)
2
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41 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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42 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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43 #end if
2
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44 hifiasm
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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45 -t \${GALAXY_SLOTS:-1}
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46 -o output
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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47 -f $filter_bits
0
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48 #if str($advanced_options.advanced_selector) == 'set':
2
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49 -k $advanced_options.hifiasm_kmer_length
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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50 -w $advanced_options.window_size
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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51 -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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52 -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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53 -r $advanced_options.correction_rounds
2
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54 #if $advanced_options.min_hist_cnt:
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55 --min-hist-cnt $advanced_options.min_hist_cnt
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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56 #end if
4
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57 --max-kocc $advanced_options.max_kocc
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58 #if $advanced_options.hg_size
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59 --hg-size $advanced_options.hg_size
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60 #end if
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61
0
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62 #end if
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63 #if str($assembly_options.assembly_selector) == 'set':
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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64 -a $assembly_options.cleaning_rounds
2
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65 -z $assembly_options.adapter_length
0
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66 -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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67 -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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68 -n $assembly_options.remove_tips
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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69 -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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70 -y $assembly_options.min_overlap
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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71 $assembly_options.disable_post_join
2
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72 $assembly_options.ignore_error_corrected
4
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73 #if $assembly_options.hom_cov
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74 --hom-cov $assembly_options.hom_cov
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
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75 #end if
0
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76 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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77 #if str($mode.mode_selector) == 'trio':
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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78 -1 hap1.yak
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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79 -2 hap2.yak
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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80 -c $mode.max_kmers
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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81 -d $mode.min_kmers
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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82 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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83 #if str($purge_options.purge_selector) == 'set':
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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84 -l $purge_options.purge_level
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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85 -s $purge_options.similarity_threshold
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86 -O $purge_options.minimum_overlap
4
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87 #if $purge_options.purge_max:
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88 --purge-max $purge_options.purge_max
0
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89 #end if
2
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90 #if $purge_options.n_hap:
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91 --n-hap $purge_options.n_hap
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92 #end if
0
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93 #end if
2
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94
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95 #if str($hic_partition.hic_partition_selector) == 'set':
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96 --h1 '${ ' '.join(["%s" % $x for $x in $hic_partition.h1]) }'
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97 --h2 '${ ' '.join(["%s" % $x for $x in $hic_partition.h2]) }'
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98 #if $hic_partition.seed:
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99 --seed $hic_partition.seed
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100 #end if
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101 #if $hic_partition.n_weight:
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102 --n-weight $hic_partition.n_weight
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103 #end if
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104 #if $hic_partition.n_perturb:
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105 --n-perturb $hic_partition.n_perturb
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106 #end if
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107 #if $hic_partition.f_perturb:
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108 --f-perturb $hic_partition.f_perturb
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109 #end if
3
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110 --l-msjoin $hic_partition.l_msjoin
2
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111 #end if
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112
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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113 ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly.
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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114 --primary
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115 $input_filenames
3
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116 #if $log_out:
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117 2> output.log
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118 #end if
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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119 ]]>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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120 </command>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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121 <inputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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122 <conditional name="mode">
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123 <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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124 <option value="standard">Standard</option>
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125 <option value="trio">Trio mode</option>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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126 </param>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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127 <when value="standard">
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128 <expand macro="reads" />
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129 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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130 <when value="trio">
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131 <expand macro="reads" />
1
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132 <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />
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133 <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />
0
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134 <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower 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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135 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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136 <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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137 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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138 </conditional>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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139 <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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140 <conditional name="advanced_options">
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141 <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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142 <option value="blank">Leave default</option>
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143 <option value="set">Specify</option>
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144 </param>
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145 <when value="blank" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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146 <when value="set">
4
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147 <param name="hifiasm_kmer_length" argument="-k" type="integer" min="0" max="64" value="51" label="Hifiasm k-mer length" />
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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148 <param name="window_size" argument="-w" type="integer" min="0" value="51" label="Minimizer window size" />
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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" />
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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" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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151 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" />
2
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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" />
4
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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" />
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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">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
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155 <sanitizer invalid_char="">
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156 <valid initial="string.digits">
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157 <add value="k" />
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158 <add value="K" />
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159 <add value="m" />
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160 <add value="M" />
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161 <add value="G" />
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162 <add value="g" />
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163 </valid>
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164 </sanitizer>
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165 <validator type="regex">[0-9kKmMGg]+</validator>
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166 </param>
0
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167 </when>
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168 </conditional>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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169
0
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170 <conditional name="assembly_options">
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171 <param name="assembly_selector" type="select" label="Assembly options">
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172 <option value="blank">Leave default</option>
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173 <option value="set">Specify</option>
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174 </param>
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175 <when value="blank" />
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176 <when value="set">
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177 <param name="cleaning_rounds" argument="-a" type="integer" value="4" label="Cleaning rounds" />
2
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178 <param name="adapter_length" argument="-z" type="integer" min="0" value="0" label="Length of adapters to be removed" />
0
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179 <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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180 <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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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" />
2
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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"/>
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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"/>
0
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184 <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" />
2
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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." />
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186 <param argument="--hom-cov" type="integer" optional="True" value="" label="Homozygous read coverage" />
0
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187 </when>
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188 </conditional>
2
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189
0
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190 <conditional name="purge_options">
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191 <param name="purge_selector" type="select" label="Options for purging duplicates">
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192 <option value="blank">Leave default</option>
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193 <option value="set">Specify</option>
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194 </param>
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195 <when value="blank" />
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196 <when value="set">
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197 <param name="purge_level" argument="-l" type="select" label="Purge level">
2
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198 <option value="0" selected="true">None (0)</option>
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199 <option value="1">Light (1)</option>
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200 <option value="2">Aggressive (2)</option>
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201 <option value="3">Aggressive - high heterozygosity rate (3)</option>
0
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202 </param>
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203 <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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204 <param name="minimum_overlap" argument="-O" type="integer" value="1" label="Minimum overlapped reads for duplicate haplotigs" />
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205 <param argument="--purge-max" type="integer" optional="true" label="Coverage upper bound" help="If not set, this will be determined automatically" />
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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." />
0
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207 </when>
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208 </conditional>
2
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209
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210 <conditional name="hic_partition">
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211 <param name="hic_partition_selector" type="select" label="Options for Hi-C-partition">
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212 <option value="blank">Leave default</option>
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213 <option value="set">Specify</option>
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214 </param>
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215 <when value="blank" />
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216 <when value="set">
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217 <param argument="--h1" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R1 reads" />
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218 <param argument="--h2" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R2 reads" />
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219 <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed" />
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220 <param argument="--n-weight" type="integer" min="1" value="" optional="true" label="Rounds of reweighting Hi-C links" />
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221 <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation" />
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222 <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation" />
3
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223 <param argument="--l-msjoin" type="integer" min="0" value="500000" label="Detect misjoined unitigs of greater than or equal to specified size" help="A value of 0 disables this filter"/>
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224 </when>
2
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225 </conditional>
3
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226 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
0
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227 </inputs>
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228 <outputs>
1
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229 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph">
0
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230 <filter>mode['mode_selector'] == 'standard'</filter>
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231 </data>
2
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232 <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}, haplotype-resolved raw unitig graph">
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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233 <filter>mode['mode_selector'] == 'trio'</filter>
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234 </data>
1
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235 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}, processed unitig graph">
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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236 <filter>mode['mode_selector'] == 'standard'</filter>
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237 </data>
1
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238 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}, primary assembly contig graph">
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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239 <filter>mode['mode_selector'] == 'standard'</filter>
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240 </data>
1
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241 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}, alternate assembly contig graph">
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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242 <filter>mode['mode_selector'] == 'standard'</filter>
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243 </data>
2
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244 <data name="hap1_contigs" format="gfa1" from_work_dir="output.hap1.p_ctg.gfa" label="${tool.name} on ${on_string}, hap1.p_ctg contig graph">
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245 <filter>mode['mode_selector'] == 'trio'</filter>
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246 </data>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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247 <data name="hap2_contigs" format="gfa1" from_work_dir="output.hap2.p_ctg.gfa" label="${tool.name} on ${on_string}, hap2.p_ctg contig graph">
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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248 <filter>mode['mode_selector'] == 'trio'</filter>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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249 </data>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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250 <!-- Hi-C partition outputs -->
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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251 <data name="hic_contig_graph" format="gfa1" from_work_dir="output.hic.p_ctg.gfa" label="${tool.name} ${on_string}, HI-C contig graph">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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252 <filter>hic_partition['hic_partition_selector'] == 'set'</filter>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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253 </data>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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254 <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.bp.hap1.p_ctg.gfa" label="${tool.name} ${on_string}, HI-C hap1 balanced contig graph hap1">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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255 <filter>hic_partition['hic_partition_selector'] == 'set'</filter>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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256 </data>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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257 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.bp.hap2.p_ctg.gfa" label="${tool.name} ${on_string}, HI-C hap2 balanced contig graph hap2">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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258 <filter>hic_partition['hic_partition_selector'] == 'set'</filter>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
259 </data>
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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260 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}, log file">
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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261 <filter>log_out</filter>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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262 </data>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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263 </outputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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264 <tests>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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265 <test>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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266 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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267 <param name="filter_bits" value="0" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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268 <param name="mode_selector" value="standard" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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269 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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270 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
271 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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272 <output name="alternate_contig_graph" ftype="gfa1">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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273 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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274 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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275 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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diff changeset
276 </output>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
277 </test>
1
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
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278 <test>
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
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279 <param name="reads" value="hifiasm-in2-0.fa.gz,hifiasm-in2-1.fa.gz,hifiasm-in2-2.fa.gz,hifiasm-in2-3.fa.gz,hifiasm-in2-4.fa.gz" ftype="fasta.gz" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
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diff changeset
280 <param name="filter_bits" value="0" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
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diff changeset
281 <param name="mode_selector" value="standard" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
parents: 0
diff changeset
282 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
parents: 0
diff changeset
283 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
parents: 0
diff changeset
284 <output name="primary_contig_graph" file="hifiasm-out2-primary.gfa" ftype="gfa1" />
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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285 <output name="alternate_contig_graph" ftype="gfa1">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
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286 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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diff changeset
287 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
288 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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289 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
290 </test>
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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291 <!-- Test logfile out-->
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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292 <test>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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diff changeset
293 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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diff changeset
294 <param name="filter_bits" value="0" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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diff changeset
295 <param name="mode_selector" value="standard" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
296 <param name="log_out" value="yes"/>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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diff changeset
297 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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diff changeset
298 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
299 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
300 <output name="alternate_contig_graph" ftype="gfa1">
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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301 <assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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diff changeset
302 <has_size value="0"/>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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303 </assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
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304 </output>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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305 <output name="log_file" ftype="txt">
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
306 <assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
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307 <has_line line="[M::main] CMD: hifiasm -t 1 -o output -f 0 --primary input_0.fasta.gz"/>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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308 </assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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diff changeset
309 </output>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
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310 </test>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
311
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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diff changeset
312 <!-- Test Hi-C
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
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diff changeset
313 <test>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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diff changeset
314 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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diff changeset
315 <param name="filter_bits" value="0" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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diff changeset
316 <param name="mode_selector" value="standard" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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diff changeset
317 <conditional name="hic_partition">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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318 <param name="hic_partition_selector" value="set"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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diff changeset
319 <param name="h1" value="r1_1.fq"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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diff changeset
320 <param name="h2" value="r2_1.fq"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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321 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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322 <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
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diff changeset
323 <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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324 <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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325 <output name="alternate_contig_graph" ftype="gfa1">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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326 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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diff changeset
327 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
328 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
329 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
330 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
331 -->
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
332 <!-- Test trio mode -->
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
333 <test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
334 <param name="filter_bits" value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
335 <conditional name="mode">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
336 <param name="mode_selector" value="trio"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
337 <param name="reads" value="child.fasta.gz"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
338 <param name="hap1_reads" value="paternal.fasta.gz"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
339 <param name="hap2_reads" value="maternal.fasta.gz"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
340 <param name="max_kmers" value="2"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
341 <param name="min_kmers" value="5"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
342 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
343 <output name="raw_unitigs_trio" ftype="gfa1">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
344 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
345 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
346 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
347 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
348 <output name="hap1_contigs">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
349 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
350 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
351 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
352 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
353 <output name="hap2_contigs">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
354 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
355 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
356 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
357 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
358 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
359 <!-- Test ignore-error-corrected option -->
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
360 <test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
361 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
362 <param name="filter_bits" value="0" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
363 <param name="mode_selector" value="standard" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
364 <conditional name="assembly_options">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
365 <param name="assembly_selector" value="set"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
366 <param name="ignore_error_corrected" value="True"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
367 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
368 <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
369 <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
370 <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
371 <output name="alternate_contig_graph" ftype="gfa1">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
372 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
373 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
374 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
375 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
376 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
377 <!-- Test expected haplotype number -->
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
378 <test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
379 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
380 <param name="filter_bits" value="0" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
381 <param name="mode_selector" value="standard" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
382 <conditional name="purge_options">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
383 <param name="purge_selector" value="set"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
384 <param name="n_hap" value="1"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
385 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
386 <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
387 <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
388 <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
389 <output name="alternate_contig_graph" ftype="gfa1">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
390 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
391 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
392 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
393 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
394 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
395 <!-- Test min_hist_cnt option -->
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
396 <test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
397 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
398 <param name="filter_bits" value="0" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
399 <param name="mode_selector" value="standard" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
400 <conditional name="advanced_options">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
401 <param name="advanced_selector" value="set"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
402 <param name="min_hist_cnt" value="1"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
403 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
404 <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
405 <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
406 <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
407 <output name="alternate_contig_graph" ftype="gfa1">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
408 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
409 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
410 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
411 </output>
1
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
parents: 0
diff changeset
412 </test>
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
413 <!-- Test max_kooc option -->
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
414 <test>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
415 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
416 <param name="filter_bits" value="0" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
417 <param name="mode_selector" value="standard" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
418 <conditional name="advanced_options">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
419 <param name="advanced_selector" value="set"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
420 <param name="max_kooc" value="21000"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
421 </conditional>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
422 <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
423 <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
424 <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
425 <output name="alternate_contig_graph" ftype="gfa1">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
426 <assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
427 <has_size value="0"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
428 </assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
429 </output>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
430 </test>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
431 <!-- Test hg-size option -->
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
432 <test>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
433 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
434 <param name="filter_bits" value="0" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
435 <param name="mode_selector" value="standard" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
436 <conditional name="advanced_options">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
437 <param name="advanced_selector" value="set"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
438 <param name="hg_size" value="1k"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
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439 </conditional>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
440 <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
441 <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
442 <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
443 <output name="alternate_contig_graph" ftype="gfa1">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
444 <assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
445 <has_size value="0"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
446 </assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
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447 </output>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
448 </test>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
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diff changeset
449 <!-- Test ignore-error-corrected option -->
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
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450 <test>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
451 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
452 <param name="filter_bits" value="0" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
453 <param name="mode_selector" value="standard" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
454 <conditional name="assembly_options">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
455 <param name="assembly_selector" value="set"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
456 <param name="hom-cov" value="1000"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
457 </conditional>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
458 <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
459 <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
460 <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
461 <output name="alternate_contig_graph" ftype="gfa1">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
462 <assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
463 <has_size value="0"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
464 </assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
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diff changeset
465 </output>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
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diff changeset
466 </test>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
467 </tests>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
468 <help><![CDATA[
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
469 ***********************************
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
470 HiFiASM - a fast de novo assembler
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
471 ***********************************
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
472
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
473 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.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
474
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
475 #### Assembly mode
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
476 - *Standard*
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
477 - *Trio* When parental short reads are available, hifiasm can generate a pair of haplotype-resolved assemblies with trio binning.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
478
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
479 #### Trio Options
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
480 - *Haplotype 1 reads* : list of hap1/paternal read names
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
481 - *Haplotype 2 reads* : list of hap2/maternal read names
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
482 - *Lower bound of the binned k-mer's frequency*
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
483 - *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"
bgruening
parents:
diff changeset
484
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
485 *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.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
486
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
487 #### Advanced options
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
488 - *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.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
489 - *K-mer length* (must be <64)
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
490 - *Minimizer window size*
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
491 - *Drop K-mers* K-mers that occur more than this value multiplied by the coverage will be discarded
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
492 - *Maximum overlaps to consider* consider up to max(-D*coverage,-N) overlaps for each oriented read
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
493 - *Correction rounds* round of correction
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
494
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
495 #### Assembly options
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
496 - *Cleaning rounds* round of assembly cleaning
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
497 - *Minimum contig bubble* size Pop contig graph bubbles smaller than this value
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
498 - *Minimum unitig bubble* size Pop unitig graph bubbles smaller than this value
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
499 - *Tip unitigs* Keep only tip unitigs with a number of reads greater than or equal to this value
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
500 - *Maximum overlap drop ratio*
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
501 - *Minimum overlap drop ratio*
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
502 - *Skip post join contigs step* disable post join contigs step which may improve N50
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
503
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
504 #### Options for purging duplicates
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
505 - *Purge level* 0: no purging; 1: light; 2: aggressive [0 for trio; 2 for unzip]
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
506 - *Similarity threshold for duplicate haplotigs*
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
507 - *Minimum overlapped reads for duplicate haplotigs*
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
508 - *Coverage upper bound* If not set, this will be determined automatically
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
509 - *Experimental high-heterozygosity mode* enable this mode for high heterozygosity sample NB: May be unstable
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
510
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
511 #### Hi-C-partition options
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
512
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
513 - *RNG seed*
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
514 - *Rounds of reweighting Hi-C links* : increasing this may improves phasing results but takes longer time.
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
515 - *Rounds of perturbation* : increasing this may improves phasing results but takes longer time.
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
516 - *Fraction to flip for perturbation* : increasing this may improves phasing results but takes longer time.
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
517
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
518 ### Outputs
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
519
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
520 Non Trio assembly
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
521 - Haplotype-resolved raw unitig graph in GFA format. This graph keeps all haplotype information, including somatic mutations and recurrent sequencing errors.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
522 - 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.
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
523 - Primary assembly contig graph : This graph collapses different haplotypes.
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
524 - Alternate assembly contig graph : This graph consists of all assemblies that are discarded in primary contig graph.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
525
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
526
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
527 Trio assembly
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
528 - Haplotype-resolved raw unitig graph in GFA format . This graph keeps all haplotype information.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
529 - Phased paternal/haplotype1 contig graph. This graph keeps the phased paternal/haplotype1 assembly.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
530 - Phased maternal/haplotype2 contig graph. This graph keeps the phased maternal/haplotype2 assembly.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
531
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
532
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
533
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
534 ]]></help>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
535 <citations>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
536 <citation type="doi">10.1038/s41592-020-01056-5</citation>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
537 </citations>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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538 </tool>