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annotate hifiasm.xml @ 19:284a1cb82b61 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
author iuc
date Thu, 11 Jul 2024 14:44:22 +0000
parents df25d4fb79b7
children 5161f204ba63
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3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
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1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
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bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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3 <macros>
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284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
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4 <token name="@TOOL_VERSION@">0.19.9</token>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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5 <token name="@VERSION_SUFFIX@">0</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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284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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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>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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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[
1
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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 #set $ultralong_inputs = list()
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25 #for idx, read in enumerate($mode.reads):
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26 #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
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27 ln -s '$read' $inputfile &&
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28 $input_files.append($inputfile)
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29 #end for
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30 #set $input_filenames = ' '.join($input_files)
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31 #if str($hic_partition.hic_partition_selector) == 'set'
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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32 mkdir HiCF HiCR &&
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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33 #for idx, read in enumerate($hic_partition.h1):
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34 #set $inputfile = './HiCF/input_%d.%s' % ($idx, $read.dataset.extension)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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35 ln -s '$read' $inputfile &&
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36 $hic1_inputs.append($inputfile)
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37 #end for
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38 #for idx, read in enumerate($hic_partition.h2):
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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39 #set $inputfile = './HiCR/input_%d.%s' % ($idx, $read.dataset.extension)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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40 ln -s '$read' $inputfile &&
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41 $hic2_inputs.append($inputfile)
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42 #end for
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43 #end if
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44 #if str($ont_integration.ont_integration_selector) == 'set'
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45 mkdir ultralong &&
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46 #for idx, read in enumerate($ont_integration.ul):
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47 #set $inputfile = './ultralong/input_%d.%s' % ($idx, $read.dataset.extension)
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48 ln -s '$read' $inputfile &&
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49 $ultralong_inputs.append($inputfile)
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50 #end for
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51 #end if
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52 #if str($mode.mode_selector) == 'trio':
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53 #if str($mode.trioinput.trio_input_selector) == 'reads':
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54 #for idx, read in enumerate($mode.trioinput.hap1_reads):
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55 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
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56 ln -s '$read' $inputfile &&
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57 $hap1_inputs.append($inputfile)
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58 #end for
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59 #for idx, read in enumerate($mode.trioinput.hap2_reads):
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60 #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
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61 ln -s '$read' $inputfile &&
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62 $hap2_inputs.append($inputfile)
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63 #end for
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64 #set $hap1_filenames = ' '.join($hap1_inputs)
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65 #set $hap2_filenames = ' '.join($hap2_inputs)
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66 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
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67 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
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68 #end if
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69 #if str($mode.trioinput.trio_input_selector) == 'lists':
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70 #set $hap1_filenames = $mode.trioinput.hap1_list
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71 #set $hap2_filenames = $mode.trioinput.hap2_list
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72 #end if
0
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73 #end if
2
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74 hifiasm
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75 -t \${GALAXY_SLOTS:-1}
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76 -o output
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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77 -f $filter_bits
0
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78 #if str($advanced_options.advanced_selector) == 'set':
2
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79 -k $advanced_options.hifiasm_kmer_length
0
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80 -w $advanced_options.window_size
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81 -D $advanced_options.drop_kmers
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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diff changeset
82 -N $advanced_options.max_overlaps
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
83 -r $advanced_options.correction_rounds
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
84 #if $advanced_options.min_hist_cnt:
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
85 --min-hist-cnt $advanced_options.min_hist_cnt
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
86 #end if
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
87 --max-kocc $advanced_options.max_kocc
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
88 #if $advanced_options.hg_size
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
89 --hg-size $advanced_options.hg_size
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
90 #end if
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
91
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
92 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
93 #if str($assembly_options.assembly_selector) == 'set':
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
94 -a $assembly_options.cleaning_rounds
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
95 -z $assembly_options.adapter_length
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
96 -m $assembly_options.pop_contigs
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
97 -p $assembly_options.pop_unitigs
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
98 -n $assembly_options.remove_tips
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
99 -x $assembly_options.max_overlap
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
100 -y $assembly_options.min_overlap
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
101 $assembly_options.disable_post_join
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
102 $assembly_options.ignore_error_corrected
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
103 #if $assembly_options.hom_cov
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
104 --hom-cov $assembly_options.hom_cov
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
105 #end if
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
106 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
107 #if str($mode.mode_selector) == 'trio':
16
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
108 #if str($mode.trioinput.trio_input_selector) == 'reads':
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
109 -1 hap1.yak
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
110 -2 hap2.yak
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
111 #end if
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
112 #if str($mode.trioinput.trio_input_selector) == 'lists':
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
113 -3 $hap1_filenames
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
114 -4 $hap2_filenames
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
115 #end if
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
116 -c $mode.max_kmers
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
117 -d $mode.min_kmers
16
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
118 $mode.trio_dual
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
119 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
120 #if str($purge_options.purge_selector) == 'set':
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
121 -l $purge_options.purge_level
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
122 -s $purge_options.similarity_threshold
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
123 -O $purge_options.minimum_overlap
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
124 #if $purge_options.purge_max:
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
125 --purge-max $purge_options.purge_max
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
126 #end if
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
127 #if $purge_options.n_hap:
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
128 --n-hap $purge_options.n_hap
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
129 #end if
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
130 #end if
15
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4
bgruening
parents: 14
diff changeset
131 #if str($scaffolding_options.scaffold_selector) == 'set':
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4
bgruening
parents: 14
diff changeset
132 --dual-scaf
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4
bgruening
parents: 14
diff changeset
133 #if $scaffolding_options.scaf_gap:
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4
bgruening
parents: 14
diff changeset
134 --scaf-gap $scaffolding_options.scaf_gap
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4
bgruening
parents: 14
diff changeset
135 #end if
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4
bgruening
parents: 14
diff changeset
136 #end if
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
137
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
138 #if str($hic_partition.hic_partition_selector) == 'set':
11
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
139 --h1 ${ ','.join(["'%s'" % $x for $x in $hic1_inputs]) }
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
140 --h2 ${ ','.join(["'%s'" % $x for $x in $hic2_inputs]) }
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
141 #if $hic_partition.seed:
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
142 --seed $hic_partition.seed
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
143 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
144 #if $hic_partition.n_weight:
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
145 --n-weight $hic_partition.n_weight
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
146 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
147 #if $hic_partition.n_perturb:
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
148 --n-perturb $hic_partition.n_perturb
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
149 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
150 #if $hic_partition.f_perturb:
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
151 --f-perturb $hic_partition.f_perturb
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
152 #end if
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
153 --l-msjoin $hic_partition.l_msjoin
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
154 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
155
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
156 #if str($ont_integration.ont_integration_selector) == 'set':
11
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
157 --ul ${ ','.join(["'%s'" % $x for $x in $ultralong_inputs]) }
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
158 #if $ont_integration.ul_rate:
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
159 --ul-rate $ont_integration.ul_rate
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
160 #end if
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
161 #if $ont_integration.ul_tip:
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
162 --ul-tip $ont_integration.ul_tip
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
163 #end if
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
164 #end if
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
165
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
166 ## 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"
bgruening
parents: 1
diff changeset
167 --primary
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
168 $input_filenames
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
169 #if $log_out:
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
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170 2> output.log
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171 #end if
12
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172
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173 && mkdir noseq_files && mv *.noseq.gfa noseq_files
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174
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175 #if $bins_out:
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176 && mkdir bin_files && mv *.bin bin_files
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177 #end if
0
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178 ]]>
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179 </command>
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180 <inputs>
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181 <conditional name="mode">
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182 <param name="mode_selector" type="select" label="Assembly mode">
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183 <option value="standard">Standard</option>
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184 <option value="trio">Trio mode</option>
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185 </param>
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186 <when value="standard">
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187 <expand macro="reads"/>
0
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188 </when>
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189 <when value="trio">
19
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190 <expand macro="reads"/>
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191 <conditional name="trioinput">
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192 <param name="trio_input_selector" type="select" label="What parental information are you using?">
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193 <option value="reads">Parental reads (FASTQ files, gzipped or otherwise)</option>
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194 <option value="lists">Lists of reads assigned by parent (text files)</option>
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195 </param>
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196 <when value="reads">
19
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197 <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads"/>
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198 <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads"/>
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199 </when>
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200 <when value="lists">
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201 <param name="hap1_list" type="data" format="txt,tabular" label="Haplotype 1 read list"/>
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202 <param name="hap2_list" type="data" format="txt,tabular" label="Haplotype 2 read list"/>
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203 </when>
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204 </conditional>
19
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205 <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency"/>
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206 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency"/>
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207 <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length"/>
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208 <param argument="--trio-dual" type="boolean" truevalue="--trio-dual" falsevalue="" label="Utilize homology information to correct trio-phasing errors"/>
0
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209 </when>
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210 </conditional>
19
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211 <param name="filter_bits" argument="-f" type="integer" min="0" value="37" label="Bits for bloom filter" help="A value of 0 disables the bloom filter"/>
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212 <conditional name="assembly_options">
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213 <param name="assembly_selector" type="select" label="Assembly options">
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214 <option value="blank">Leave default</option>
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215 <option value="set">Specify</option>
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216 </param>
19
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217 <when value="blank"/>
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218 <when value="set">
19
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219 <param name="cleaning_rounds" argument="-a" type="integer" value="4" label="Cleaning rounds"/>
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220 <param name="adapter_length" argument="-z" type="integer" min="0" value="0" label="Length of adapters to be removed"/>
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221 <param name="pop_contigs" argument="-m" type="integer" value="10000000" label="Minimum contig bubble size" help="Pop contig graph bubbles smaller than this value"/>
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222 <param name="pop_unitigs" argument="-p" type="integer" value="100000" label="Minimum unitig bubble size" help="Pop unitig graph bubbles smaller than this value"/>
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223 <param name="remove_tips" argument="-n" type="integer" value="3" label="Tip unitigs" help="Keep only tip unitigs with a number of reads greater than or equal to this value"/>
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224 <param name="max_overlap" argument="-x" type="float" min="0" max="1" value="0.8" label="Maximum overlap drop ratio" help="This option is used with -r. Given a node N in the assembly graph, let max(N) be the length of the largest overlap of N. Hifiasm iteratively drops overlaps of N if their length/max(N) are below a threshold controlled by -x. Hifiasm applies -r rounds of short overlap removal with an increasing threshold between -x and -y"/>
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225 <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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226 <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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227 <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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228 <param argument="--hom-cov" type="integer" optional="True" value="" label="Homozygous read coverage"/>
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229 </when>
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230 </conditional>
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231 <conditional name="purge_options">
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232 <param name="purge_selector" type="select" label="Options for purging duplicates">
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233 <option value="blank">Leave default</option>
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234 <option value="set">Specify</option>
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235 </param>
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236 <when value="blank"/>
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237 <when value="set">
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238 <param name="purge_level" argument="-l" type="select" label="Purge level">
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239 <option value="0" selected="true">None (0)</option>
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240 <option value="1">Light (1)</option>
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241 <option value="2">Aggressive (2)</option>
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242 <option value="3">Aggressive - high heterozygosity rate (3)</option>
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243 </param>
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244 <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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245 <param name="minimum_overlap" argument="-O" type="integer" value="1" label="Minimum overlapped reads for duplicate haplotigs"/>
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246 <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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247 <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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248 </when>
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249 </conditional>
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250 <conditional name="hic_partition">
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251 <param name="hic_partition_selector" type="select" label="Options for Hi-C-partition">
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252 <option value="blank">Leave default</option>
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253 <option value="set">Specify</option>
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254 </param>
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255 <when value="blank"/>
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256 <when value="set">
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257 <param argument="--h1" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R1 reads"/>
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258 <param argument="--h2" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R2 reads"/>
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259 <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed"/>
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260 <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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261 <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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262 <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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263 <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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264 </when>
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265 </conditional>
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266 <conditional name="ont_integration">
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267 <param name="ont_integration_selector" type="select" label="Options for ONT integration">
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268 <option value="blank">Leave default</option>
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269 <option value="set">Specify</option>
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270 </param>
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271 <when value="blank"/>
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272 <when value="set">
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273 <param argument="--ul" type="data" format="fastq,fastq.gz,fasta,fasta.gz" multiple="true" label="Ultra-long (>100kb) reads"/>
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274 <param argument="--ul-rate" type="float" value="0.2" optional="true" label="error rate of ultra-long reads (default 0.2)"/>
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275 <param argument="--ul-tip" type="integer" value="6" optional="true" label="remove tip unitigs composed of less than (INT) reads for the UL assembly (default 6)"/>
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276 </when>
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277 </conditional>
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278 <conditional name="advanced_options">
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279 <param name="advanced_selector" type="select" label="Advanced options">
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280 <option value="blank">Leave default</option>
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281 <option value="set">Specify</option>
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282 </param>
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283 <when value="blank"/>
0
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284 <when value="set">
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285 <param name="hifiasm_kmer_length" argument="-k" type="integer" min="0" max="64" value="51" label="Hifiasm k-mer length"/>
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286 <param name="window_size" argument="-w" type="integer" min="0" value="51" label="Minimizer window size"/>
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287 <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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288 <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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289 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds"/>
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290 <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"/>
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291 <param argument="--max-kocc" type="integer" min="0" value="20000" label="Maximum k-mer ocurrence" help="Employ k-mers occurring less than INT times to rescue repetitive overlaps"/>
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292 <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size"
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293 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">
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294 <sanitizer invalid_char="">
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295 <valid initial="string.digits">
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296 <add value="k"/>
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297 <add value="K"/>
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298 <add value="m"/>
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299 <add value="M"/>
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300 <add value="G"/>
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301 <add value="g"/>
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302 </valid>
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303 </sanitizer>
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304 <validator type="regex">[0-9kKmMGg]+</validator>
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305 </param>
0
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306 </when>
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307 </conditional>
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308 <conditional name="scaffolding_options">
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309 <param name="scaffold_selector" type="select" label="Options for hifiasm scaffolding">
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310 <option value="blank">No scaffolding (default)</option>
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311 <option value="set">Turn on hifiasm scaffolding</option>
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312 </param>
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313 <when value="blank"/>
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314 <when value="set">
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315 <param argument="--scaf-gap" type="integer" min="1" value="3000000" optional="true" label="Max scaffolding gap size" help="Set the max gap size of scaffolds (default is 3,000,000)"/>
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316 </when>
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317 </conditional>
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318 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
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319 <param name="bins_out" type="boolean" label="Output .bin files (used for development and debugging)?" truevalue="yes" falsevalue="no"/>
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320 </inputs>
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321 <outputs>
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322 <!--Standard mode-->
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323 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for pseudohaplotype assembly">
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324 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
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325 </data>
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326 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph for pseudohaplotype assembly">
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327 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
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328 </data>
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329 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph for pseudohaplotype assembly">
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330 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0
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331 </data>
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332 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph for pseudohaplotype assembly">
5
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333 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0
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334 </data>
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335 <!--Trio outputs without Hi-c reads-->
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336 <data name="hap1_contigs" format="gfa1" from_work_dir="output.dip.hap1.p_ctg.gfa" label="${tool.name} on ${on_string}: hap1.p_ctg contig graph">
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337 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0
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338 </data>
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339 <data name="hap2_contigs" format="gfa1" from_work_dir="output.dip.hap2.p_ctg.gfa" label="${tool.name} on ${on_string}: hap2.p_ctg contig graph">
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340 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
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341 </data>
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342 <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for HiC-phased assembly">
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343 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0
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344 </data>
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345 <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph for HiC-phased assembly">
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346 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
2
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347 </data>
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348 <!-- Stardand mode with Hi-C partition outputs -->
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349 <data name="hic_pcontig_graph" format="gfa1" from_work_dir="output.hic.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C primary contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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350 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
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351 </data>
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352 <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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353 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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354 </data>
6
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355 <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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356 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
0
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357 </data>
6
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358 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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359 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
2
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360 </data>
7
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361 <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig">
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4
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362 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
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363 </data>
5
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364 <!--Trio outputs with Hi-c reads-->
11
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365 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw unitig graph">
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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366 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
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367 </data>
11
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368 <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed unitig graph">
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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369 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
0
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370 </data>
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371 <!--Log, noseq, and bin output-->
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
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372 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
3
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373 <filter>log_out</filter>
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374 </data>
9
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375 <collection name="noseq_files" type="list" label="${tool.name} on ${on_string}: noseq files">
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376 <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files"/>
8
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377 </collection>
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378 <collection name="bin_files" type="list" label="${tool.name} on ${on_string}: bin files">
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
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379 <filter>bins_out</filter>
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380 <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="bin_files"/>
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381 </collection>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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382 </outputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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383 <tests>
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384 <!-- TEST 1 -->
8
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385 <test expect_num_outputs="5">
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386 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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387 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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388 <param name="mode_selector" value="standard"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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389 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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390 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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391 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1"/>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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392 </test>
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393 <!-- TEST 2 -->
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394 <test expect_num_outputs="5">
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diff changeset
395 <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"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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396 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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397 <param name="mode_selector" value="standard"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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398 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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parents: 18
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399 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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400 <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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401 </test>
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402 <!-- TEST 3: Test logfile out-->
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diff changeset
403 <test expect_num_outputs="6">
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diff changeset
404 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
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diff changeset
405 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
406 <param name="mode_selector" value="standard"/>
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
407 <param name="log_out" value="yes"/>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
408 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
409 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
410 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1"/>
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
411 <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
412 <assert_contents>
9
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024
bgruening
parents: 8
diff changeset
413 <has_text text="-o output -f 0 --primary input_0.fasta.gz"/>
3
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
414 </assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
415 </output>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947"
bgruening
parents: 2
diff changeset
416 </test>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
417 <!--TEST 4: Test Hi-C reads-->
8
5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
bgruening
parents: 7
diff changeset
418 <test expect_num_outputs="6">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
419 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
420 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
421 <param name="mode_selector" value="standard"/>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
422 <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
423 <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
424 <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
425 <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
426 <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
427 <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
428 <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
429 <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
430 </conditional>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
431 <output name="hic_pcontig_graph" file="hifiasm-out-hifi-p.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
432 <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1"/>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
433 <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
434 <assert_contents>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
435 <has_text_matching expression="^S"/>
9
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024
bgruening
parents: 8
diff changeset
436 <has_size value="83914" delta="500"/>
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
437 </assert_contents>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
438 </output>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
439 <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
440 <assert_contents>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
441 <has_text_matching expression="^S"/>
9
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024
bgruening
parents: 8
diff changeset
442 <has_size value="83914" delta="500"/>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
443 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
444 </output>
7
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4
bgruening
parents: 6
diff changeset
445 <output name="hic_raw_initig" ftype="gfa1" >
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4
bgruening
parents: 6
diff changeset
446 <assert_contents>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
447 <has_text_matching expression="^S"/>
9
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024
bgruening
parents: 8
diff changeset
448 <has_size value="83904" delta="500"/>
7
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4
bgruening
parents: 6
diff changeset
449 </assert_contents>
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4
bgruening
parents: 6
diff changeset
450 </output>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
451 </test>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
452 <!-- TEST 5: Test trio mode -->
8
5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
bgruening
parents: 7
diff changeset
453 <test expect_num_outputs="5">
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
454 <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
455 <conditional name="mode">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
456 <param name="mode_selector" value="trio"/>
16
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
457 <param name="trio_input_selector" value="reads"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
458 <conditional name="trioinput">
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
459 <param name="reads" value="child.fasta.gz"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
460 <param name="hap1_reads" value="paternal.fasta.gz"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
461 <param name="hap2_reads" value="maternal.fasta.gz"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
462 </conditional>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
463 <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
464 <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
465 </conditional>
9
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024
bgruening
parents: 8
diff changeset
466 <assert_command>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
467 <has_text text="-1 hap1.yak"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
468 <has_text text="-2 hap2.yak"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
469 <has_text text="--primary"/>
9
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024
bgruening
parents: 8
diff changeset
470 </assert_command>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
471 </test>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
472 <!-- TEST 6: Test ignore-error-corrected option -->
8
5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
bgruening
parents: 7
diff changeset
473 <test expect_num_outputs="5">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
474 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
475 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
476 <param name="mode_selector" value="standard"/>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
477 <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
478 <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
479 <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
480 </conditional>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
481 <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
482 <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
483 <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1"/>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
484 </test>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
485 <!-- TEST 7: Test expected haplotype number -->
8
5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
bgruening
parents: 7
diff changeset
486 <test expect_num_outputs="5">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
487 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
488 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
489 <param name="mode_selector" value="standard"/>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
490 <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
491 <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
492 <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
493 </conditional>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
494 <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
495 <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
496 <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1"/>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
497 </test>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
498 <!-- TEST 8: Test min_hist_cnt option -->
8
5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
bgruening
parents: 7
diff changeset
499 <test expect_num_outputs="5">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
500 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
501 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
502 <param name="mode_selector" value="standard"/>
2
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0"
bgruening
parents: 1
diff changeset
503 <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
504 <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
505 <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
506 </conditional>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
507 <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
508 <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
509 <output name="primary_contig_graph" file="hifiasm-out5-primary.gfa" ftype="gfa1"/>
1
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85"
bgruening
parents: 0
diff changeset
510 </test>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
511 <!-- TEST 9: Test max_kooc option -->
8
5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
bgruening
parents: 7
diff changeset
512 <test expect_num_outputs="5">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
513 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
514 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
515 <param name="mode_selector" value="standard"/>
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
516 <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
517 <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
518 <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
519 </conditional>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
520 <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
521 <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
522 <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1"/>
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
523 </test>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
524 <!-- TEST 10: Test hg-size option -->
8
5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
bgruening
parents: 7
diff changeset
525 <test expect_num_outputs="5">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
526 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
527 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
528 <param name="mode_selector" value="standard"/>
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
529 <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
530 <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
531 <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
532 </conditional>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
533 <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
534 <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
535 <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1"/>
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
536 </test>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
537 <!-- TEST 11: Test ignore-error-corrected option -->
8
5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed
bgruening
parents: 7
diff changeset
538 <test expect_num_outputs="5">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
539 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
540 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
541 <param name="mode_selector" value="standard"/>
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
542 <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
543 <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
544 <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
545 </conditional>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
546 <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
547 <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
548 <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1"/>
4
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962"
bgruening
parents: 3
diff changeset
549 </test>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
550 <!-- TEST 12: test nanopore input -->
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
551 <test expect_num_outputs="5">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
552 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
553 <param name="mode_selector" value="standard"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
554 <param name="filter_bits" value="0"/>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
555 <conditional name="ont_integration">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
556 <param name="ont_integration_selector" value="set"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
557 <param name="ul" value="nanopore.fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
558 <param name="ul_tip" value="1"/>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
559 </conditional>
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
560 <output name="primary_contig_graph" file="hifiasm-out11-primary.gfa" ftype="gfa1"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
561 <output name="raw_unitigs" file="hifiasm-out11-raw.gfa" ftype="gfa1"/>
11
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
562 </test>
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
563 <!-- TEST 13: test multi-file nanopore input -->
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
564 <test expect_num_outputs="6">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
565 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
566 <param name="mode_selector" value="standard"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
567 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
568 <param name="log_out" value="yes"/>
11
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
569 <conditional name="ont_integration">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
570 <param name="ont_integration_selector" value="set"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
571 <param name="ul" value="nanopore.fasta.gz,nanopore.fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
572 <param name="ul_tip" value="1"/>
11
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
573 </conditional>
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
574 <output name="log_file" ftype="txt">
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
575 <assert_contents>
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
576 <has_text text="--ul ./ultralong/input_0.fasta.gz,./ultralong/input_1.fasta.gz"/>
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
577 </assert_contents>
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f
bgruening
parents: 10
diff changeset
578 </output>
10
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa
bgruening
parents: 9
diff changeset
579 </test>
12
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
580 <!-- TEST 14: test bin files -->
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
581 <test expect_num_outputs="6">
19
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
582 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
583 <param name="filter_bits" value="0"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
584 <param name="mode_selector" value="standard"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
585 <param name="bins_out" value="yes"/>
284a1cb82b61 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 47637031b6d38391762d49ee5c8317810aa8d766
iuc
parents: 18
diff changeset
586 <output_collection name="bin_files" type="list" count="3"/>
12
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
587 </test>
16
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
588 <!-- TEST 15: Test trio LIST mode -->
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
589 <test expect_num_outputs="6">
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
590 <param name="filter_bits" value="0"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
591 <param name="log_out" value="yes"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
592 <conditional name="mode">
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
593 <param name="mode_selector" value="trio"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
594 <param name="reads" value="child.fasta.gz"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
595 <conditional name="trioinput">
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
596 <param name="trio_input_selector" value="lists"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
597 <param name="hap1_list" value="maternal.headers.txt"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
598 <param name="hap2_list" value="paternal.headers.txt"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
599 </conditional>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
600 <param name="max_kmers" value="2"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
601 <param name="min_kmers" value="5"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
602 </conditional>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
603 <output name="log_file" ftype="txt">
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
604 <assert_contents>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
605 <has_text text="flagged 100 reads, out of 100 lines in file"/>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
606 </assert_contents>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
607 </output>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5
bgruening
parents: 15
diff changeset
608 </test>
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
609 </tests>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
610 <help><![CDATA[
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
611 .. class:: infomark
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
612
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
613 **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
614
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
615
12
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
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diff changeset
616 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.
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
617
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
618 ----
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
619
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
620 .. class:: infomark
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
621
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
622 **Assembly mode**
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
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diff changeset
623
12
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
624 - *Standard*: Standard assembly can be run in pseudohaplotype mode, or with Hi-C phasing using Hi-C reads from the same individual.
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
625 - *Trio*: When parental short reads are available, hifiasm can generate a pair of haplotype-resolved assemblies with trio binning.
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
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diff changeset
626
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
627 ----
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
628
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
629 .. class:: infomark
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
630
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
631 **Outputs**
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
632
12
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
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diff changeset
633 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
634
12
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
635 - Haplotype-resolved raw unitig graph: This graph keeps all haplotype information, including somatic mutations and recurrent sequencing errors.
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
636 - Haplotype-resolved processed unitig graph without small bubbles: This graph 'pops' small bubbles in the raw unitig graph; small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information.
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
637 - Primary assembly contig graph: This graph includes a complete assembly with long stretches of phased blocks, though there may be some haplotype collapse.
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
638 - Alternate assembly contig graph: This graph consists of all contigs that are discarded from the primary contig graph.
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa
bgruening
parents: 11
diff changeset
639 - [hap1]/[hap2] contig graph: Each graph consists of phased contigs (output only with Hi-C phasing enabled).
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
640
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
641
5
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
642 Trio assembly:
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a"
bgruening
parents: 4
diff changeset
643
0
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
644 - 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
645 - 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
646 - 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
647
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
648
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
649 ]]></help>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
650 <citations>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
parents:
diff changeset
651 <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
652 </citations>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a"
bgruening
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diff changeset
653 </tool>