hifiasm: hifiasm.xml annotate

annotate hifiasm.xml @ 9:c388a21dcbf1 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024

author	bgruening
date	Fri, 20 Jan 2023 22:27:43 +0000
parents	5f625c63b8bc
children	2061fb3b81b4

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>
9 c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	4 <token name="@TOOL_VERSION@">0.18.5</token>
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	5 <token name="@VERSION_SUFFIX@">0</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 $hic2_inputs = list()
1 6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	24 #for idx, read in enumerate($mode.reads):
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	25 #set $inputfile = 'input_%d.%s' % ($idx, $read.dataset.extension)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	26 ln -s '$read' $inputfile &&
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	27 $input_files.append($inputfile)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	28 #end for
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	29 #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	30 #if str($hic_partition.hic_partition_selector) == 'set'
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	31 mkdir HiCF HiCR &&
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	32 #for idx, read in enumerate($hic_partition.h1):
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	33 #set $inputfile = './HiCF/input_%d.%s' % ($idx, $read.dataset.extension)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	34 ln -s '$read' $inputfile &&
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	35 $hic1_inputs.append($inputfile)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	36 #end for
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	37 #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	38 #set $inputfile = './HiCR/input_%d.%s' % ($idx, $read.dataset.extension)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	39 ln -s '$read' $inputfile &&
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	40 $hic2_inputs.append($inputfile)
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	41 #end for
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	42 #end if
1 6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	43 #if str($mode.mode_selector) == 'trio':
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	44 #for idx, read in enumerate($mode.hap1_reads):
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	45 #set $inputfile = 'hap1_input_%d.%s' % ($idx, $read.dataset.extension)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	46 ln -s '$read' $inputfile &&
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	47 $hap1_inputs.append($inputfile)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	48 #end for
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	49 #for idx, read in enumerate($mode.hap2_reads):
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	50 #set $inputfile = 'hap2_input_%d.%s' % ($idx, $read.dataset.extension)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	51 ln -s '$read' $inputfile &&
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	52 $hap2_inputs.append($inputfile)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	53 #end for
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	54 #set $hap1_filenames = ' '.join($hap1_inputs)
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	55 #set $hap2_filenames = ' '.join($hap2_inputs)
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	56 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap1.yak $hap1_filenames &&
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	57 yak count -k$mode.yak_kmer_length -b$filter_bits -t\${GALAXY_SLOTS:-1} -o hap2.yak $hap2_filenames &&
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	58 #end if
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	59 hifiasm
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	60 -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	61 -o output
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	62 -f $filter_bits
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	63 #if str($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	64 -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	65 -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	66 -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	67 -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	68 -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	69 #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	70 --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	71 #end if
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	72 --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	73 #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	74 --hg-size $advanced_options.hg_size
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	75 #end if
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	76
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	77 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	78 #if str($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	79 -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	80 -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	81 -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	82 -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	83 -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	84 -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	85 -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	86 $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	87 $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	88 #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	89 --hom-cov $assembly_options.hom_cov
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	90 #end if
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	91 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	92 #if str($mode.mode_selector) == 'trio':
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	93 -1 hap1.yak
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	94 -2 hap2.yak
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	95 -c $mode.max_kmers
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	96 -d $mode.min_kmers
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	97 #end if
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	98 #if str($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	99 -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	100 -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	101 -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	102 #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	103 --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	104 #end if
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	105 #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	106 --n-hap $purge_options.n_hap
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	107 #end if
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	108 #end if
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	109
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	110 #if str($hic_partition.hic_partition_selector) == 'set':
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	111 --h1 '${ ' '.join(["%s" % $x for $x in $hic1_inputs]) }'
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	112 --h2 '${ ' '.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	113 #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	114 --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	115 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	116 #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	117 --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	118 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	119 #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	120 --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	121 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	122 #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	123 --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	124 #end if
3 9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	125 --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	126 #end if
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	127
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	128 ## Changed the default outputs of hifiasm. Hifiasm outputs a primary assembly and two balanced haplotypes in default. Incorporated the option '--primary' to output primary assembly and alternate assembly.
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	129 --primary
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	130 $input_filenames
3 9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	131 #if $log_out:
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	132 2> output.log
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	133 #end if
8 5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed bgruening parents: 7 diff changeset	134 && mkdir noseq_files && mv *.noseq.gfa noseq_files
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	135 ]]>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	136 </command>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	137 <inputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	138 <conditional name="mode">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	139 <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	140 <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	141 <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	142 </param>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	143 <when value="standard">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	144 <expand macro="reads" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	145 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	146 <when value="trio">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	147 <expand macro="reads" />
1 6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	148 <param name="hap1_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 1 reads" />
6505bd37670d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1122ef1b9a407a781d1416d07b272016d16a6a85" bgruening parents: 0 diff changeset	149 <param name="hap2_reads" type="data" format="fastq,fastq.gz" multiple="true" label="Haplotype 2 reads" />
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	150 <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	151 <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	152 <param name="yak_kmer_length" type="integer" min="0" max="64" value="31" label="Yak counter k-mer length" />
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	153 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	154 </conditional>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	155 <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	156 <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	157 <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	158 <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	159 <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	160 </param>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	161 <when value="blank" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	162 <when value="set">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	163 <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	164 <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	165 <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	166 <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	167 <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	168 <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	169 <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	170 <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	171 <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	172 <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	173 </when>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	174 </conditional>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	175 <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	176 <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	177 <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	178 <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	179 </param>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	180 <when value="blank" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	181 <when value="set">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	182 <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	183 <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	184 <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	185 <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	186 <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	187 </param>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	188 <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	189 <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	190 <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	191 <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	192 </when>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	193 </conditional>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	194 <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	195 <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	196 <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	197 <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	198 </param>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	199 <when value="blank" />
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	200 <when value="set">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	201 <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	202 <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	203 <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	204 <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	205 <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	206 <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	207 <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	208 </when>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	209 </conditional>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	210 <conditional name="advanced_options">
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	211 <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	212 <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	213 <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	214 </param>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	215 <when value="blank" />
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	216 <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	217 <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	218 <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	219 <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	220 <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	221 <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	222 <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	223 <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	224 <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	225 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	226 <sanitizer invalid_char="">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	227 <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	228 <add value="k" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	229 <add value="K" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	230 <add value="m" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	231 <add value="M" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	232 <add value="G" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	233 <add value="g" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	234 </valid>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	235 </sanitizer>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	236 <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	237 </param>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	238 </when>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	239 </conditional>
3 9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	240 <param name="log_out" type="boolean" label="Output log file?" 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	241 </inputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	242 <outputs>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	243 <!--Standard mode-->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	244 <data name="raw_unitigs" format="gfa1" from_work_dir="output.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	245 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	246 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	247 <data name="processed_unitigs" format="gfa1" from_work_dir="output.p_utg.gfa" label="${tool.name} on ${on_string}: processed unitig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	248 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	249 </data>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	250 <data name="primary_contig_graph" format="gfa1" from_work_dir="output.p_ctg.gfa" label="${tool.name} on ${on_string}: primary assembly contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	251 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	252 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	253 <data name="alternate_contig_graph" format="gfa1" from_work_dir="output.a_ctg.gfa" label="${tool.name} on ${on_string}: alternate assembly contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	254 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	255 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	256 <!--Trio outputs without Hi-c reads-->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	257 <data name="hap1_contigs" format="gfa1" from_work_dir="output.dip.hap1.p_ctg.gfa" label="${tool.name} on ${on_string}: hap1.p_ctg contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	258 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	259 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	260 <data name="hap2_contigs" format="gfa1" from_work_dir="output.dip.hap2.p_ctg.gfa" label="${tool.name} on ${on_string}: hap2.p_ctg contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	261 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	262 </data>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	263 <data name="raw_unitigs_trio" format="gfa1" from_work_dir="output.dip.r_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved raw unitig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	264 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	265 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	266 <data name="processed_unitigs_trio" format="gfa1" from_work_dir="output.dip.p_utg.gfa" label="${tool.name} on ${on_string}: haplotype-resolved processed unitig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	267 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'blank'</filter>
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	268 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	269 <!-- Stardand mode with Hi-C partition outputs -->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	270 <data name="hic_pcontig_graph" format="gfa1" from_work_dir="output.hic.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C primary contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	271 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	272 </data>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	273 <data name="hic_acontig_graph" format="gfa1" from_work_dir="output.hic.a_ctg.gfa" label="${tool.name} ${on_string}: Hi-C alternate contig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	274 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	275 </data>
6 5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 diff changeset	276 <data name="hic_balanced_contig_hap1_graph" format="gfa1" from_work_dir="output.hic.hap1.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap1 balanced contig graph hap1">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	277 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	278 </data>
6 5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 diff changeset	279 <data name="hic_balanced_contig_hap2_graph" format="gfa1" from_work_dir="output.hic.hap2.p_ctg.gfa" label="${tool.name} ${on_string}: Hi-C hap2 balanced contig graph hap2">
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	280 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	281 </data>
7 366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 diff changeset	282 <data name="hic_raw_initig" format="gfa1" from_work_dir="output.hic.r_utg.gfa" label="${tool.name} ${on_string}: Hi-C raw unitig">
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 diff changeset	283 <filter>mode['mode_selector'] == 'standard' and hic_partition['hic_partition_selector'] == 'set'</filter>
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 diff changeset	284 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	285 <!--Trio outputs with Hi-c reads-->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	286 <data name="hap1_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.r_utg.gfa" label="${tool.name} on ${on_string}: raw initig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	287 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	288 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	289 <data name="hap2_contigs_hic" format="gfa1" from_work_dir="output.hic.bench.p_utg.gfa" label="${tool.name} on ${on_string}: processsed initig graph">
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	290 <filter>mode['mode_selector'] == 'trio' and hic_partition['hic_partition_selector'] == 'set'</filter>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	291 </data>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	292 <!--Log output-->
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	293 <data name="log_file" format="txt" from_work_dir="output.log" label="${tool.name} ${on_string}: log file">
3 9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	294 <filter>log_out</filter>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	295 </data>
9 c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	296 <collection name="noseq_files" type="list" label="${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	297 <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	298 </collection>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	299 </outputs>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	300 <tests>
8 5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed bgruening parents: 7 diff changeset	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 </test>
8 5f625c63b8bc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 10f1ab4414ebb4693bfb7a7ded4633e393009bed bgruening parents: 7 diff changeset	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 <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	316 </test>
3 9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	317 <!-- 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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <assert_contents>
9 c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	328 <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	329 </assert_contents>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	330 </output>
9ef6920c3089 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 7132f1d3fddf9c07282e69b3c0d5c71f61d24947" bgruening parents: 2 diff changeset	331 </test>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	332 <!--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	333 <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	334 <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	335 <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	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345 </conditional>
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	346 <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	347 <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	348 <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	349 <assert_contents>
6 5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 diff changeset	350 <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	351 <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	352 </assert_contents>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	353 </output>
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	354 <output name="hic_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	355 <assert_contents>
6 5bec28269d95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 6817ef65c64c0800e21815822c38beba52075f75" bgruening parents: 5 diff changeset	356 <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	357 <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	358 </assert_contents>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	359 </output>
7 366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 diff changeset	360 <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	361 <assert_contents>
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 diff changeset	362 <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	363 <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	364 </assert_contents>
366a11d316a7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit e11987ed5bffa0f2aa60d28acfb9301ac87d4dc4 bgruening parents: 6 diff changeset	365 </output>
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	366 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	367 <!-- 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	368 <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	369 <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	370 <conditional name="mode">
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	371 <param name="mode_selector" value="trio"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	372 <param name="reads" value="child.fasta.gz"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	373 <param name="hap1_reads" value="paternal.fasta.gz"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	374 <param name="hap2_reads" value="maternal.fasta.gz"/>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	375 <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	376 <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	377 </conditional>
9 c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	378 <assert_command>
c388a21dcbf1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 590539b6db0f8ef16d31c2023a22aa97143bf024 bgruening parents: 8 diff changeset	379 <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	380 <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	381 <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	382 </assert_command>
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	383 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	384 <!-- 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	385 <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	386 <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	387 <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	388 <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	389 <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	390 <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	391 <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	392 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	393 <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	394 <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	395 <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	396 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	397 <!-- 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	398 <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	399 <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	400 <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	401 <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	402 <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	403 <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	404 <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	405 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	406 <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	407 <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	408 <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	409 </test>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	410 <!-- 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	411 <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	412 <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	413 <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	414 <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	415 <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	416 <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	417 <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	418 </conditional>
f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	419 <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	420 <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	421 <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	422 </test>
4 3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	423 <!-- 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	424 <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	425 <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	426 <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	427 <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	428 <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	429 <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	430 <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	431 </conditional>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	432 <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	433 <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	434 <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	435 </test>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	436 <!-- 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	437 <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	438 <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	439 <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	440 <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	441 <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	442 <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	443 <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	444 </conditional>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	445 <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	446 <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	447 <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	448 </test>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	449 <!-- 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	450 <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	451 <param name="reads" value="hifiasm-in1.fa.gz" ftype="fasta.gz" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	452 <param name="filter_bits" value="0" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	453 <param name="mode_selector" value="standard" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	454 <conditional name="assembly_options">
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	455 <param name="assembly_selector" value="set"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	456 <param name="hom-cov" value="1000"/>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	457 </conditional>
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	458 <output name="raw_unitigs" file="hifiasm-out8-raw.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	459 <output name="processed_unitigs" file="hifiasm-out8-processed.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	460 <output name="primary_contig_graph" file="hifiasm-out8-primary.gfa" ftype="gfa1" />
3f7be05a1597 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 8d76914ac4407512b1691a1ddd3d95dda6c80962" bgruening parents: 3 diff changeset	461 </test>
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	462 </tests>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	463 <help><![CDATA[
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	464 .. class:: infomark
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	465
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	466 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	467
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	468
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	469 Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	470
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	471 ----
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	472
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	473 .. class:: infomark
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	474
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	475 Assembly mode
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	476
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	477 - Standard
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	478 - Trio When parental short reads are available, hifiasm can generate a pair of haplotype-resolved assemblies with trio binning.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	479
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	480 ----
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	481
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	482 .. class:: infomark
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	483
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	484 Outputs
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	485
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	486 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	487
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	488 - Haplotype-resolved raw unitig graph in GFA format. This graph keeps all haplotype information, including somatic mutations and recurrent sequencing errors.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	489 - Haplotype-resolved processed unitig graph without small bubbles : Small bubbles might be caused by somatic mutations or noise in data, which are not the real haplotype information.
2 f3c89da3af16 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 5a03c44d52d545bd23e651bfba1cc73050eec9a0" bgruening parents: 1 diff changeset	490 - Primary assembly contig graph : This graph collapses different haplotypes.
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	491 - Alternate assembly contig graph : This graph consists of all assemblies that are discarded in primary contig graph.
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	492
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	493
5 045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	494 Trio assembly:
045c7c3d8e59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit 1e4c6c2e48f5e95beed75bb76134cbf7fa55dc8a" bgruening parents: 4 diff changeset	495
0 bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	496 - 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	497 - 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	498 - 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	499
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	500
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	501 ]]></help>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	502 <citations>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	503 <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	504 </citations>
bf0a4667e3ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit a118fad06e94683813e214af107fedd5fd80500a" bgruening parents: diff changeset	505 </tool>

Mercurial > repos > bgruening > hifiasm

annotate hifiasm.xml @ 9:c388a21dcbf1 draft