hifiasm: hifiasm.xml annotate

annotate hifiasm.xml @ 16:41cea2aa2dce draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5

author	bgruening
date	Fri, 20 Oct 2023 22:03:32 +0000
parents	60024a528cbd
children	0ee0c3089254

rev	line source
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	1 <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	2 <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	3 <macros>
15 60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	4 <token name="@TOOL_VERSION@">0.19.7</token>
16 41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	5 <token name="@VERSION_SUFFIX@">1</token>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	6 <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	7 <xml name="reads">
1 6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	8 <param name="reads" type="data" format="@FORMATS@" multiple="true" label="Input reads" />
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	9 </xml>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	10 </macros>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	11 <requirements>
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	12 <requirement type="package" version="@TOOL_VERSION@">hifiasm</requirement>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	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" bgruening parents: diff changeset	14 </requirements>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	15 <version_command>hifiasm --version</version_command>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	16 <command detect_errors="exit_code">
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	17
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	18 <![CDATA[
1 6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	19 #set $input_files = list()
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	20 #set $hap1_inputs = list()
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	21 #set $hap2_inputs = list()
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	22 #set $hic1_inputs = list()
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	23 #set $hic2_inputs = list()
10 2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	24 #set $ultralong_inputs = list()
1 6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	25 #for idx, read in enumerate($mode.reads):
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	26 #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	27 ln -s '$read' $inputfile &&
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	28 $input_files.append($inputfile)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	29 #end for
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	30 #set $input_filenames = ' '.join($input_files)
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	31 #if str($hic_partition.hic_partition_selector) == 'set'
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	32 mkdir HiCF HiCR &&
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	33 #for idx, read in enumerate($hic_partition.h1):
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	34 #set $inputfile = './HiCF/input_%d.%s' % ($idx, $read.dataset.extension)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	35 ln -s '$read' $inputfile &&
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	36 $hic1_inputs.append($inputfile)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	37 #end for
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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" bgruening parents: 4 diff changeset	39 #set $inputfile = './HiCR/input_%d.%s' % ($idx, $read.dataset.extension)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	40 ln -s '$read' $inputfile &&
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	41 $hic2_inputs.append($inputfile)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	42 #end for
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	43 #end if
10 2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	44 #if str($ont_integration.ont_integration_selector) == 'set'
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	45 mkdir ultralong &&
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	46 #for idx, read in enumerate($ont_integration.ul):
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	47 #set $inputfile = './ultralong/input_%d.%s' % ($idx, $read.dataset.extension)
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	48 ln -s '$read' $inputfile &&
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	49 $ultralong_inputs.append($inputfile)
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	50 #end for
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	51 #end if
1 6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	52 #if str($mode.mode_selector) == 'trio':
16 41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	53 #if str($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	54 #for idx, read in enumerate($mode.trioinput.hap1_reads):
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	55 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	56 ln -s '$read' $inputfile &&
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	57 $hap1_inputs.append($inputfile)
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	58 #end for
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	59 #for idx, read in enumerate($mode.trioinput.hap2_reads):
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	60 #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	61 ln -s '$read' $inputfile &&
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	62 $hap2_inputs.append($inputfile)
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	63 #end for
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	64 #set $hap1_filenames = ' '.join($hap1_inputs)
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	65 #set $hap2_filenames = ' '.join($hap2_inputs)
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	66 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	67 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	68 #end if
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	69 #if str($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	70 #set $hap1_filenames = $mode.trioinput.hap1_list
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	71 #set $hap2_filenames = $mode.trioinput.hap2_list
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	72 #end if
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	73 #end if
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	74 hifiasm
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	75 -t \${GALAXY_SLOTS:-1}
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	76 -o output
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	77 -f $filter_bits
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	78 #if str($advanced_options.advanced_selector) == 'set':
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	79 -k $advanced_options.hifiasm_kmer_length
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	80 -w $advanced_options.window_size
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	81 -D $advanced_options.drop_kmers
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: 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" bgruening parents: 2 diff changeset	170 2> output.log
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	171 #end if
12 da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	172
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	173 && mkdir noseq_files && mv *.noseq.gfa noseq_files
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	174
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	175 #if $bins_out:
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	176 && mkdir bin_files && mv *.bin bin_files
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	177 #end if
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	178 ]]>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	179 </command>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	180 <inputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	181 <conditional name="mode">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	182 <param name="mode_selector" type="select" label="Assembly mode">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	183 <option value="standard">Standard</option>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	184 <option value="trio">Trio mode</option>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	185 </param>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	186 <when value="standard">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	187 <expand macro="reads" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	188 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	189 <when value="trio">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	190 <expand macro="reads" />
16 41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	191 <conditional name="trioinput">
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	192 <param name="trio_input_selector" type="select" label="What parental information are you using?">
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	193 <option value="reads">Parental reads (FASTQ files, gzipped or otherwise)</option>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	194 <option value="lists">Lists of reads assigned by parent (text files)</option>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	195 </param>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	196 <when value="reads">
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	197 <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	198 <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	199 </when>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	200 <when value="lists">
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	201 <param name="hap1_list" type="data" format="txt,tabular" label="Haplotype 1 read list" />
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	202 <param name="hap2_list" type="data" format="txt,tabular" label="Haplotype 2 read list" />
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	203 </when>
41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	204 </conditional>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	205 <param name="max_kmers" argument="-c" type="integer" value="2" label="Lower bound of the binned k-mer's frequency" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	206 <param name="min_kmers" argument="-d" type="integer" value="5" label="Upper bound of the binned k-mer's frequency" />
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	207 <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />
16 41cea2aa2dce planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7dca92baf6a91f10bced28b883f14d3f4d7630c5 bgruening parents: 15 diff changeset	208 <param name="trio_dual" argument="--trio-dual" type="boolean" truevalue="--trio-dual" falsevalue="" label="Utilize homology information to correct trio-phasing errors" />
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	209 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	210 </conditional>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	212 <conditional name="assembly_options">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	213 <param name="assembly_selector" type="select" label="Assembly options">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	214 <option value="blank">Leave default</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	215 <option value="set">Specify</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	216 </param>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	217 <when value="blank" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	218 <when value="set">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	219 <param name="cleaning_rounds" argument="-a" type="integer" value="4" label="Cleaning rounds" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	220 <param name="adapter_length" argument="-z" type="integer" min="0" value="0" label="Length of adapters to be removed" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	226 <param name="disable_post_join" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Skip post join contigs step" help="May improve N50" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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." />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	228 <param argument="--hom-cov" type="integer" optional="True" value="" label="Homozygous read coverage" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	229 </when>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	230 </conditional>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	231 <conditional name="purge_options">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	232 <param name="purge_selector" type="select" label="Options for purging duplicates">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	233 <option value="blank">Leave default</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	234 <option value="set">Specify</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	235 </param>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	236 <when value="blank" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	237 <when value="set">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	238 <param name="purge_level" argument="-l" type="select" label="Purge level">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	239 <option value="0" selected="true">None (0)</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	240 <option value="1">Light (1)</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	241 <option value="2">Aggressive (2)</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	242 <option value="3">Aggressive - high heterozygosity rate (3)</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	243 </param>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	244 <param name="similarity_threshold" argument="-s" type="float" min="0" max="1" value="0.75" label="Similarity threshold for duplicate haplotigs" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	245 <param name="minimum_overlap" argument="-O" type="integer" value="1" label="Minimum overlapped reads for duplicate haplotigs" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	246 <param argument="--purge-max" type="integer" optional="true" label="Coverage upper bound" help="If not set, this will be determined automatically" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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." />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	248 </when>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	249 </conditional>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	250 <conditional name="hic_partition">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	251 <param name="hic_partition_selector" type="select" label="Options for Hi-C-partition">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	252 <option value="blank">Leave default</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	253 <option value="set">Specify</option>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	254 </param>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	255 <when value="blank" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	256 <when value="set">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	257 <param argument="--h1" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R1 reads" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	258 <param argument="--h2" type="data" format="fastq,fastq.gz" multiple="true" label="Hi-C R2 reads" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	259 <param argument="--seed" type="integer" min="1" value="" optional="true" label="RNG seed" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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"/>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	264 </when>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	265 </conditional>
10 2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	266 <conditional name="ont_integration">
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	267 <param name="ont_integration_selector" type="select" label="Options for ONT integration">
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	268 <option value="blank">Leave default</option>
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	269 <option value="set">Specify</option>
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	270 </param>
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	271 <when value="blank" />
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	272 <when value="set">
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	273 <param argument="--ul" type="data" format="fastq,fastq.gz,fasta,fasta.gz" multiple="true" label="Ultra-long (>10kb) reads" />
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	274 <param argument="--ul-rate" type="float" value="0.2" optional="true" label="error rate of ultra-long reads (default 0.2)" />
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	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)" />
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	276 </when>
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	277 </conditional>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	278 <conditional name="advanced_options">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	279 <param name="advanced_selector" type="select" label="Advanced options">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	280 <option value="blank">Leave default</option>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	281 <option value="set">Specify</option>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	282 </param>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	283 <when value="blank" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	284 <when value="set">
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	285 <param name="hifiasm_kmer_length" argument="-k" type="integer" min="0" max="64" value="51" label="Hifiasm k-mer length" />
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	286 <param name="window_size" argument="-w" type="integer" min="0" value="51" label="Minimizer window size" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	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" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	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" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	289 <param name="correction_rounds" argument="-r" type="integer" value="3" label="Correction rounds" />
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	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" />
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	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" />
6 5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 diff changeset	292 <param argument="--hg-size" type="text" value="" optional="true" label="Estimated haploid genome size"
5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 diff changeset	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">
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	294 <sanitizer invalid_char="">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	295 <valid initial="string.digits">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	296 <add value="k" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	297 <add value="K" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	298 <add value="m" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	299 <add value="M" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	300 <add value="G" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	301 <add value="g" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	302 </valid>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	303 </sanitizer>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	304 <validator type="regex">[0-9kKmMGg]+</validator>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	305 </param>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	306 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	307 </conditional>
15 60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	308 <conditional name="scaffolding_options">
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	309 <param name="scaffold_selector" type="select" label="Options for hifiasm scaffolding">
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	310 <option value="blank">No scaffolding (default)</option>
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	311 <option value="set">Turn on hifiasm scaffolding</option>
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	312 </param>
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	313 <when value="blank" />
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	314 <when value="set">
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	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)" />
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	316 </when>
60024a528cbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4 bgruening parents: 14 diff changeset	317 </conditional>
12 da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	318 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no" />
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	319 <param name="bins_out" type="boolean" label="Output .bin files (used for development and debugging)?" truevalue="yes" falsevalue="no" />
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	320 </inputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	321 <outputs>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	322 <!--Standard mode-->
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	323 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for pseudohaplotype assembly">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	324 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	325 </data>
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	326 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph for pseudohaplotype assembly">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	327 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	328 </data>
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	329 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph for pseudohaplotype assembly">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	330 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	331 </data>
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	332 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph for pseudohaplotype assembly">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	333 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	334 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	335 <!--Trio outputs without Hi-c reads-->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	336 <data name="hap1_contigs" format="gfa1" from_work_dir="output.dip.hap1.p_ctg.gfa" label="${tool.name} on ${on_string}: hap1.p_ctg contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	337 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	338 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	339 <data name="hap2_contigs" format="gfa1" from_work_dir="output.dip.hap2.p_ctg.gfa" label="${tool.name} on ${on_string}: hap2.p_ctg contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	340 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	341 </data>
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	342 <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph for HiC-phased assembly">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	343 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	344 </data>
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	345 <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph for HiC-phased assembly">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	346 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	347 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	348 <!-- Stardand mode with Hi-C partition outputs -->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	349 <data name="hic_pcontig_graph" format="gfa1" from_work_dir="output.hic.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C primary contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	350 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	351 </data>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	352 <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	353 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	354 </data>
6 5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 diff changeset	355 <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	356 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	357 </data>
6 5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 diff changeset	358 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	359 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	360 </data>
7 366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 diff changeset	361 <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig">
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 diff changeset	362 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 diff changeset	363 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	364 <!--Trio outputs with Hi-c reads-->
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	365 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw unitig graph">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	366 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	367 </data>
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	368 <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed unitig graph">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	369 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	370 </data>
12 da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	371 <!--Log, noseq, and bin output-->
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	372 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
3 9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	373 <filter>log_out</filter>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	374 </data>
9 c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	375 <collection name="noseq_files" type="list" label="${tool.name} on ${on_string}: noseq files">
8 5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed bgruening parents: 7 diff changeset	376 <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="noseq_files" />
5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed bgruening parents: 7 diff changeset	377 </collection>
12 da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	378 <collection name="bin_files" type="list" label="${tool.name} on ${on_string}: bin files">
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	379 <filter>bins_out</filter>
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	380 <discover_datasets pattern="__name_and_ext__" format="gfa1" directory="bin_files" />
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	381 </collection>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	382 </outputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	383 <tests>
10 2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	384 <!-- TEST 1 -->
8 5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed bgruening parents: 7 diff changeset	385 <test expect_num_outputs="5">
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	386 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	387 <param name="filter_bits" value="0" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	388 <param name="mode_selector" value="standard" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	389 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	390 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	391 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	392 </test>
10 2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	393 <!-- TEST 2 -->
8 5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed bgruening parents: 7 diff changeset	394 <test expect_num_outputs="5">
1 6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 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" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	396 <param name="filter_bits" value="0" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	397 <param name="mode_selector" value="standard" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	398 <output name="raw_unitigs" file="hifiasm-out2-raw.gfa" ftype="gfa1" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	399 <output name="processed_unitigs" file="hifiasm-out2-processed.gfa" ftype="gfa1" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	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" bgruening parents: 1 diff changeset	401 </test>
10 2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	402 <!-- TEST 3: Test logfile out-->
8 5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed bgruening parents: 7 diff changeset	403 <test expect_num_outputs="6">
3 9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	404 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	405 <param name="filter_bits" value="0" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	406 <param name="mode_selector" value="standard" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	407 <param name="log_out" value="yes"/>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	408 <output name="raw_unitigs" file="hifiasm-out1-raw.gfa" ftype="gfa1" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	409 <output name="processed_unitigs" file="hifiasm-out1-processed.gfa" ftype="gfa1" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	410 <output name="primary_contig_graph" file="hifiasm-out1-primary.gfa" ftype="gfa1" />
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	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">
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	419 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	420 <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	421 <param name="mode_selector" value="standard" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	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>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	431 <output name="hic_pcontig_graph" file="hifiasm-out-hifi-p.gfa" ftype="gfa1" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	432 <output name="hic_acontig_graph" file="hifiasm-out-hifi-a.gfa" ftype="gfa1" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	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>
6 5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 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>
6 5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 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>
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 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>
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	467 <has_text text="-1 hap1.yak" />
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	468 <has_text text="-2 hap2.yak" />
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	469 <has_text text="--primary" />
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">
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	474 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	475 <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	476 <param name="mode_selector" value="standard" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	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>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	481 <output name="raw_unitigs" file="hifiasm-out3-raw.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	482 <output name="processed_unitigs" file="hifiasm-out3-processed.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	483 <output name="primary_contig_graph" file="hifiasm-out3-primary.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	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">
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	487 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	488 <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	489 <param name="mode_selector" value="standard" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	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>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	494 <output name="raw_unitigs" file="hifiasm-out4-raw.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	495 <output name="processed_unitigs" file="hifiasm-out4-processed.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	496 <output name="primary_contig_graph" file="hifiasm-out4-primary.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	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">
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	500 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	501 <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	502 <param name="mode_selector" value="standard" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	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>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	507 <output name="raw_unitigs" file="hifiasm-out5-raw.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	508 <output name="processed_unitigs" file="hifiasm-out5-processed.gfa" ftype="gfa1" />
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	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">
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	513 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	514 <param name="filter_bits" value="0" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	515 <param name="mode_selector" value="standard" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	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>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	520 <output name="raw_unitigs" file="hifiasm-out6-raw.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	521 <output name="processed_unitigs" file="hifiasm-out6-processed.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	522 <output name="primary_contig_graph" file="hifiasm-out6-primary.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	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">
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	526 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	527 <param name="filter_bits" value="0" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	528 <param name="mode_selector" value="standard" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	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>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	533 <output name="raw_unitigs" file="hifiasm-out7-raw.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	534 <output name="processed_unitigs" file="hifiasm-out7-processed.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	535 <output name="primary_contig_graph" file="hifiasm-out7-primary.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	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">
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	539 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	540 <param name="filter_bits" value="0" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	541 <param name="mode_selector" value="standard" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	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>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	546 <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	547 <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	548 <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	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">
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	552 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	553 <param name="mode_selector" value="standard" />
12 da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 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">
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	556 <param name="ont_integration_selector" value="set" />
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	557 <param name="ul" value="nanopore.fasta.gz" />
10 2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	558 <param name="ul_tip" value="1" />
2061fb3b81b4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 0fb623fa67741a34587f9e5b110f22f68f0b59fa bgruening parents: 9 diff changeset	559 </conditional>
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	560 <output name="primary_contig_graph" file="hifiasm-out11-primary.gfa" ftype="gfa1" />
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	561 <output name="raw_unitigs" file="hifiasm-out11-raw.gfa" ftype="gfa1" />
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">
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	565 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	566 <param name="mode_selector" value="standard" />
12 da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	567 <param name="filter_bits" value="0" />
11 cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	568 <param name="log_out" value="yes" />
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">
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	570 <param name="ont_integration_selector" value="set" />
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	571 <param name="ul" value="nanopore.fasta.gz,nanopore.fasta.gz" />
cd7936c5a9a5 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit c8948d0cc178c85b078e8789304831cee5b3fa9f bgruening parents: 10 diff changeset	572 <param name="ul_tip" value="1" />
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">
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	582 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	583 <param name="filter_bits" value="0" />
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	584 <param name="mode_selector" value="standard" />
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	585 <param name="bins_out" value="yes" />
da9d8bf98802 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 2bb01c64e79df856fbcb12afde62f7c14a5f59fa bgruening parents: 11 diff changeset	586 <output_collection name="bin_files" type="list" count="3" />
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 parents: 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 parents: 11 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 parents: 4 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" bgruening parents: 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 parents: 11 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 parents: diff changeset	653 </tool>

Mercurial > repos > bgruening > hifiasm

annotate hifiasm.xml @ 16:41cea2aa2dce draft