annotate hifiasm.xml @ 6:5bec28269d95 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"
author bgruening
date Sat, 12 Feb 2022 17:15:48 +0000
parents 045c7c3d8e59
children
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1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.16.1</token>
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5 <token name="@VERSION_SUFFIX@">2</token>
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6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
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7 <xml name="reads">
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8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
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9 </xml>
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10 </macros>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">hifiasm</requirement>
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13 <requirement type="package" version="0.1">yak</requirement>
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14 </requirements>
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15 <version_command>hifiasm --version</version_command>
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16 <command detect_errors="exit_code">
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17
0
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18 <![CDATA[
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19 #set $input_files = list()
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20 #set $hap1_inputs = list()
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21 #set $hap2_inputs = list()
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22 #set $hic1_inputs = list()
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23 #set $hic2_inputs = list()
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24 #for idx, read in enumerate($mode.reads):
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25 #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension)
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26 ln -s '$read' $inputfile &&
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27 $input_files.append($inputfile)
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28 #end for
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29 #set $input_filenames = ' '.join($input_files)
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30 #if str($hic_partition.hic_partition_selector) == 'set'
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31 mkdir HiCF HiCR &&
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32 #for idx, read in enumerate($hic_partition.h1):
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33 #set $inputfile = './HiCF/input_%d.%s' % ($idx, $read.dataset.extension)
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34 ln -s '$read' $inputfile &&
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35 $hic1_inputs.append($inputfile)
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36 #end for
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37 #for idx, read in enumerate($hic_partition.h2):
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38 #set $inputfile = './HiCR/input_%d.%s' % ($idx, $read.dataset.extension)
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39 ln -s '$read' $inputfile &&
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40 $hic2_inputs.append($inputfile)
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41 #end for
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42 #end if
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43 #if str($mode.mode_selector) == 'trio':
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44 #for idx, read in enumerate($mode.hap1_reads):
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45 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
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46 ln -s '$read' $inputfile &&
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47 $hap1_inputs.append($inputfile)
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48 #end for
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49 #for idx, read in enumerate($mode.hap2_reads):
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50 #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
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51 ln -s '$read' $inputfile &&
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52 $hap2_inputs.append($inputfile)
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53 #end for
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54 #set $hap1_filenames = ' '.join($hap1_inputs)
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55 #set $hap2_filenames = ' '.join($hap2_inputs)
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56 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
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57 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
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58 #end if
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59 hifiasm
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60 -t \${GALAXY_SLOTS:-1}
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61 -o output
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62 -f $filter_bits
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63 #if str($advanced_options.advanced_selector) == 'set':
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64 -k $advanced_options.hifiasm_kmer_length
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65 -w $advanced_options.window_size
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66 -D $advanced_options.drop_kmers
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67 -N $advanced_options.max_overlaps
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68 -r $advanced_options.correction_rounds
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69 #if $advanced_options.min_hist_cnt:
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70 --min-hist-cnt $advanced_options.min_hist_cnt
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71 #end if
4
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72 --max-kocc $advanced_options.max_kocc
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73 #if $advanced_options.hg_size
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74 --hg-size $advanced_options.hg_size
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75 #end if
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76
0
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77 #end if
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78 #if str($assembly_options.assembly_selector) == 'set':
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79 -a $assembly_options.cleaning_rounds
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80 -z $assembly_options.adapter_length
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81 -m $assembly_options.pop_contigs
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82 -p $assembly_options.pop_unitigs
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83 -n $assembly_options.remove_tips
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84 -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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85 -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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86 $assembly_options.disable_post_join
2
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87 $assembly_options.ignore_error_corrected
4
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88 #if $assembly_options.hom_cov
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89 --hom-cov $assembly_options.hom_cov
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90 #end if
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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91 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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92 #if str($mode.mode_selector) == 'trio':
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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93 -1 hap1.yak
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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94 -2 hap2.yak
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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95 -c $mode.max_kmers
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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96 -d $mode.min_kmers
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97 #end if
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98 #if str($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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99 -l $purge_options.purge_level
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100 -s $purge_options.similarity_threshold
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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101 -O $purge_options.minimum_overlap
4
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102 #if $purge_options.purge_max:
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103 --purge-max $purge_options.purge_max
0
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104 #end if
2
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105 #if $purge_options.n_hap:
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106 --n-hap $purge_options.n_hap
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107 #end if
0
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108 #end if
2
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109
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110 #if str($hic_partition.hic_partition_selector) == 'set':
5
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111 --h1 '${ ' '.join(["%s" % $x for $x in $hic1_inputs]) }'
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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112 --h2 '${ ' '.join(["%s" % $x for $x in $hic2_inputs]) }'
2
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113 #if $hic_partition.seed:
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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114 --seed $hic_partition.seed
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115 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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116 #if $hic_partition.n_weight:
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117 --n-weight $hic_partition.n_weight
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118 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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119 #if $hic_partition.n_perturb:
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120 --n-perturb $hic_partition.n_perturb
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121 #end if
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122 #if $hic_partition.f_perturb:
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123 --f-perturb $hic_partition.f_perturb
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124 #end if
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
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125 --l-msjoin $hic_partition.l_msjoin
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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126 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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127
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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128 ## 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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129 --primary
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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130 $input_filenames
3
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131 #if $log_out:
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132 2> output.log
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
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133 #end if
0
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134 ]]>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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135 </command>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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136 <inputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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137 <conditional name="mode">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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138 <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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139 <option value="standard">Standard</option>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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140 <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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141 </param>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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142 <when value="standard">
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143 <expand macro="reads" />
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144 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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145 <when value="trio">
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146 <expand macro="reads" />
1
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147 <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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148 <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />
0
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149 <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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150 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
2
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151 <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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152 </when>
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153 </conditional>
5
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154 <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" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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155 <conditional name="assembly_options">
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156 <param name="assembly_selector" type="select" label="Assembly options">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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157 <option value="blank">Leave default</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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158 <option value="set">Specify</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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159 </param>
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160 <when value="blank" />
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161 <when value="set">
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162 <param name="cleaning_rounds" argument="-a" type="integer" value="4" label="Cleaning rounds" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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163 <param name="adapter_length" argument="-z" type="integer" min="0" value="0" label="Length of adapters to be removed" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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164 <param name="pop_contigs" argument="-m" type="integer" value="10000000" label="Minimum contig bubble size" help="Pop contig graph bubbles smaller than this value" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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165 <param name="pop_unitigs" argument="-p" type="integer" value="100000" label="Minimum unitig bubble size" help="Pop unitig graph bubbles smaller than this value" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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166 <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" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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167 <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"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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168 <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"/>
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169 <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" />
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170 <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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171 <param argument="--hom-cov" type="integer" optional="True" value="" label="Homozygous read coverage" />
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172 </when>
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173 </conditional>
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174 <conditional name="purge_options">
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175 <param name="purge_selector" type="select" label="Options for purging duplicates">
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176 <option value="blank">Leave default</option>
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177 <option value="set">Specify</option>
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178 </param>
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179 <when value="blank" />
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180 <when value="set">
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181 <param name="purge_level" argument="-l" type="select" label="Purge level">
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182 <option value="0" selected="true">None (0)</option>
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183 <option value="1">Light (1)</option>
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184 <option value="2">Aggressive (2)</option>
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185 <option value="3">Aggressive - high heterozygosity rate (3)</option>
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186 </param>
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187 <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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188 <param name="minimum_overlap" argument="-O" type="integer" value="1" label="Minimum overlapped reads for duplicate haplotigs" />
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189 <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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190 <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." />
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191 </when>
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192 </conditional>
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193 <conditional name="hic_partition">
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194 <param name="hic_partition_selector" type="select" label="Options for Hi-C-partition">
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195 <option value="blank">Leave default</option>
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196 <option value="set">Specify</option>
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197 </param>
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198 <when value="blank" />
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199 <when value="set">
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200 <param argument="--h1" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R1 reads" />
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201 <param argument="--h2" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R2 reads" />
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202 <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed" />
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203 <param argument="--n-weight" type="integer" min="1" value="" optional="true" label="Rounds of reweighting Hi-C links. Increasing this may improves phasing results but takes longer time" />
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204 <param argument="--n-perturb" type="integer" min="1" value="" optional="true" label="Rounds of perturbation. Increasing this may improves phasing results but takes longer time" />
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205 <param argument="--f-perturb" type="float" min="0" max="1" value="" optional="true" label="Fraction to flip for perturbation. Increasing this may improves phasing results but takes longer time" />
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206 <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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207 </when>
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208 </conditional>
0
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209 <conditional name="advanced_options">
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210 <param name="advanced_selector" type="select" label="Advanced options">
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211 <option value="blank">Leave default</option>
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212 <option value="set">Specify</option>
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213 </param>
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214 <when value="blank" />
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215 <when value="set">
4
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216 <param name="hifiasm_kmer_length" argument="-k" type="integer" min="0" max="64" value="51" label="Hifiasm k-mer length" />
0
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217 <param name="window_size" argument="-w" type="integer" min="0" value="51" label="Minimizer window size" />
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218 <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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219 <param name="max_overlaps" argument="-N" type="integer" value="100" label="Maximum overlaps to consider" help="The software selects the larger of this value and the k-mer count multiplied by coverage" />
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220 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" />
2
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221 <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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222 <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" />
6
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223 <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size"
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224 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">
4
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225 <sanitizer invalid_char="">
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226 <valid initial="string.digits">
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227 <add value="k" />
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228 <add value="K" />
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229 <add value="m" />
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230 <add value="M" />
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231 <add value="G" />
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232 <add value="g" />
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233 </valid>
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234 </sanitizer>
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235 <validator type="regex">[0-9kKmMGg]+</validator>
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236 </param>
0
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237 </when>
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238 </conditional>
3
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239 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
0
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240 </inputs>
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241 <outputs>
5
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242 <!--Standard mode-->
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243 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph">
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244 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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245 </data>
5
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246 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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247 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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248 </data>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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249 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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250 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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251 </data>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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252 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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253 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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254 </data>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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255 <!--Trio outputs without Hi-c reads-->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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256 <data name="hap1_contigs" format="gfa1" from_work_dir="output.dip.hap1.p_ctg.gfa" label="${tool.name} on ${on_string}: hap1.p_ctg contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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257 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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258 </data>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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259 <data name="hap2_contigs" format="gfa1" from_work_dir="output.dip.hap2.p_ctg.gfa" label="${tool.name} on ${on_string}: hap2.p_ctg contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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260 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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261 </data>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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262 <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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263 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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264 </data>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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265 <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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266 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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267 </data>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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268 <!-- Stardand mode with Hi-C partition outputs -->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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269 <data name="hic_pcontig_graph" format="gfa1" from_work_dir="output.hic.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C primary contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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270 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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271 </data>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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272 <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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273 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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274 </data>
6
5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"
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275 <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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276 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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277 </data>
6
5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"
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278 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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279 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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280 </data>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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281 <!--Trio outputs with Hi-c reads-->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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282 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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283 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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284 </data>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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285 <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed initig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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286 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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287 </data>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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288 <!--Log output-->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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289 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
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290 <filter>log_out</filter>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
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291 </data>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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292 </outputs>
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293 <tests>
5
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294 <test expect_num_outputs="4">
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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295 <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"
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296 <param name="filter_bits" value="0" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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297 <param name="mode_selector" value="standard" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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298 <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"
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299 <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"
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300 <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"
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301 <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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302 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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303 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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304 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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305 </output>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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306 </test>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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307 <test expect_num_outputs="4">
1
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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308 <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"
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309 <param name="filter_bits" value="0" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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310 <param name="mode_selector" value="standard" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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311 <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"
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312 <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"
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313 <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"
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314 <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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315 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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316 <has_size value="0"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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317 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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diff changeset
318 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
319 </test>
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
320 <!-- Test logfile out-->
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
321 <test expect_num_outputs="5">
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
322 <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
parents: 2
diff changeset
323 <param name="filter_bits" value="0" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
324 <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
325 <param name="log_out" value="yes"/>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
326 <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
parents: 2
diff changeset
327 <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
328 <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
329 <output name="alternate_contig_graph" ftype="gfa1">
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
330 <assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
331 <has_size value="0"/>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
332 </assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
333 </output>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
334 <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
335 <assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
336 <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
parents: 2
diff changeset
337 </assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
338 </output>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
339 </test>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
340 <!--Test Hi-C reads-->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
341 <test expect_num_outputs="4">
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
342 <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
343 <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
344 <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
345 <conditional name="hic_partition">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
346 <param name="hic_partition_selector" value="set"/>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
347 <param name="h1" value="hic_1.fastq.gz"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
348 <param name="h2" value="hic_2.fastq.gz"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
349 <param name="n_weight" value="1"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
350 <param name="n_perturb" value="1"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
351 <param name="l_perturb" value="0"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
352 <param name="l_msjoin" value="0"/>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
353 </conditional>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
354 <output name="hic_pcontig_graph" file="hifiasm-out-hifi-p.gfa" ftype="gfa1" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
355 <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
356 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
357 <assert_contents>
6
5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"
bgruening
parents: 5
diff changeset
358 <has_text_matching expression="^S" />
5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"
bgruening
parents: 5
diff changeset
359 <has_size value="59529" delta="500"/>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
360 </assert_contents>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
361 </output>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
362 <output name="hic_balanced_contig_hap1_graph" ftype="gfa1" >
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
363 <assert_contents>
6
5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"
bgruening
parents: 5
diff changeset
364 <has_text_matching expression="^S" />
5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75"
bgruening
parents: 5
diff changeset
365 <has_size value="59529" delta="500"/>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
366 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
367 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
368 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
369 <!-- Test trio mode -->
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
370 <test expect_num_outputs="4">
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
371 <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
372 <conditional name="mode">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
373 <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
374 <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
375 <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
376 <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
377 <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
378 <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
379 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
380 <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
381 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
382 <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
383 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
384 </output>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
385 <output name="processed_unitigs_trio" ftype="gfa1">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
386 <assert_contents>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
387 <has_size value="0"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
388 </assert_contents>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
389 </output>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
390 <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
391 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
392 <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
393 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
394 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
395 <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
396 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
397 <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
398 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
399 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
400 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
401 <!-- Test ignore-error-corrected option -->
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
402 <test expect_num_outputs="4">
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
403 <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
404 <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
405 <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
406 <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
407 <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
408 <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
409 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
410 <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
411 <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
412 <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
413 <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
414 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
415 <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
416 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
417 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
418 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
419 <!-- Test expected haplotype number -->
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
420 <test expect_num_outputs="4">
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
421 <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
422 <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
423 <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
424 <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
425 <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
426 <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
427 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
428 <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
429 <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
430 <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
431 <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
432 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
433 <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
434 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
435 </output>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
436 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
437 <!-- Test min_hist_cnt option -->
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
438 <test expect_num_outputs="4">
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
439 <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
440 <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
441 <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
442 <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
443 <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
444 <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
445 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
446 <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
447 <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
448 <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
449 <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
450 <assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
451 <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
452 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
453 </output>
1
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
parents: 0
diff changeset
454 </test>
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
455 <!-- Test max_kooc option -->
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
456 <test expect_num_outputs="4">
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
457 <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
458 <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
459 <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
460 <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
461 <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
462 <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
463 </conditional>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
464 <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
465 <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
466 <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
467 <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
468 <assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
469 <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
470 </assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
471 </output>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
472 </test>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
473 <!-- Test hg-size option -->
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
474 <test expect_num_outputs="4">
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
475 <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
476 <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
477 <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
478 <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
479 <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
480 <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
diff changeset
481 </conditional>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
482 <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
483 <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
484 <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
485 <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
486 <assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
487 <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
488 </assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
489 </output>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
490 </test>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
491 <!-- Test ignore-error-corrected option -->
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
492 <test expect_num_outputs="4">
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
493 <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
494 <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
495 <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
496 <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
497 <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
498 <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
499 </conditional>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
500 <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
501 <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
502 <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
503 <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
504 <assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
505 <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
506 </assert_contents>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
507 </output>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
508 </test>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
509 </tests>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
510 <help><![CDATA[
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
511 .. class:: infomark
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
512
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
513 **HiFiASM - a fast de novo assembler**
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
514
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
515
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
516 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
517
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
518 ----
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
519
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
520 .. class:: infomark
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
521
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
522 **Assembly mode**
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
523
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
524 - *Standard*
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
525 - *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
526
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
527 ----
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
528
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
529 .. class:: infomark
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
530
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
531 **Outputs**
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
532
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
533 Non Trio assembly:
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
534
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
535 - 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
536 - 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
537 - 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
538 - 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
539
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
540
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
541 Trio assembly:
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
542
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
543 - 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
544 - 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
545 - 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
546
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
547
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
548 ]]></help>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
549 <citations>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
550 <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
551 </citations>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
552 </tool>