flye: flye.xml annotate

annotate flye.xml @ 11:291923e6f276 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e

author	bgruening
date	Mon, 18 Mar 2024 12:44:09 +0000
parents	cb8dfd28c16f
children

rev	line source
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	1 <tool id="flye" name="Flye" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	2 <description>de novo assembler for single molecule sequencing reads</description>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	3 <macros>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	4 <import>macros.xml</import>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	5 </macros>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	6 <expand macro="edam_ontology"/>
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	7 <expand macro="xrefs"/>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	8 <expand macro="requirements" />
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	9 <version_command>flye --version</version_command>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	10 <command detect_errors="exit_code"><![CDATA[
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	11 #for $counter, $input in enumerate($inputs):
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	12 #if $input.is_of_type('fastqsanger', 'fastq'):
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	13 #set $ext = 'fastq'
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	14 #elif $input.is_of_type('fastqsanger.gz', 'fastq.gz'):
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	15 #set $ext = 'fastq.gz'
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	16 #elif $input.is_of_type('fasta.gz'):
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	17 #set $ext = 'fasta.gz'
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	18 #elif $input.is_of_type('fasta'):
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	19 #set $ext = 'fasta'
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	20 #end if
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	21 ln -sf '$input' ./input_${counter}.${ext} &&
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	22 #end for
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	23 flye
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	24 $mode_conditional.mode
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	25 #for $counter, $input in enumerate($inputs):
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	26 ./input_${counter}.$ext
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	27 #end for
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	28 -o out_dir
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	29 -t \${GALAXY_SLOTS:-4}
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	30 -i $iterations
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	31 #if $mode_conditional.mode == '--pacbio-hifi' and $mode_conditional.hifi_error:
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	32 --hifi-error $mode_conditional.hifi_error
1 cd256484eb1a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 6cd5f829f985631f0e8360d66a73206389101171 bgruening parents: 0 diff changeset	33 #end if
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	34 #if $min_overlap:
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	35 -m $min_overlap
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	36 #end if
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	37 #if $asm.asm_select == 'true':
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	38 --asm-coverage $asm.asm_coverage
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	39 -g '${asm.genome_size}'
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	40 #end if
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	41 $meta
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	42 $scaffold
10 cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	43 $no_alt_contigs
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	44 ]]></command>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	45 <inputs>
1 cd256484eb1a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 6cd5f829f985631f0e8360d66a73206389101171 bgruening parents: 0 diff changeset	46 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	47 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	48 <param name="mode" type="select" label="Mode">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	49 <option value="--nano-raw">Nanopore raw (--nano-raw)</option>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	50 <option value="--nano-corr">Nanopore corrected (--nano-corr)</option>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	51 <option value="--nano-hq">Nanopore HQ (--nano-hq)</option>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	52 <option value="--pacbio-raw">PacBio raw (--pacbio-raw)</option>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	53 <option value="--pacbio-corr">PacBio corrected (--pacbio-corr)</option>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	54 <option value="--pacbio-hifi">PacBio HiFi (--pacbio-hifi)</option>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	55 </param>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	56 <when value="--nano-raw"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	57 <when value="--nano-corr"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	58 <when value="--nano-hq"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	59 <when value="--pacbio-raw"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	60 <when value="--pacbio-corr"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	61 <when value="--pacbio-hifi">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	62 <param argument="--hifi-error" type="float" min="0" max="1" optional="true" label="Expected HiFi reads error rate" help="Default: 0.01"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	63 </when>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	64 </conditional>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	65 <param argument="--iterations" type="integer" value="1" label="Number of polishing iterations"
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	66 help="Polishing is performed as the final assembly stage. By default, Flye runs one polishing iteration. Additional iterations
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	67 might correct a small number of extra errors (due to improvements on how reads may align to the corrected assembly). If the
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	68 parameter is set to 0, the polishing is not performed"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	69 <param argument="--min-overlap" type="integer" min="1000" max="10000" optional="true" label="Minimum overlap between reads"
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	70 help="This sets a minimum overlap length for two reads to be considered overlapping. By default it is chosen
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	71 automatically based on the read length distribution (reads N90) and does not require manual setting. Typical
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	72 value is 3k-5k (and down to 1k for datasets with shorter read length). Intuitively, we want to set this
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	73 parameter as high as possible, so the repeat graph is less tangled. However, higher values might lead to assembly gaps.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	74 In some rare cases it makes sense to manually increase minimum overlap for assemblies of big genomes with long reads and high coverage." />
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	75 <param argument="--keep-haplotypes" type="boolean" truevalue="--keep-haplotypes" falsevalue="" checked="False" label="Keep haplotypes"
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	76 help="By default, Flye collapses graph structures caused by alternative haplotypes (bubbles, superbubbles, roundabouts) to produce longer
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	77 consensus contigs. This option retains the alternative paths on the graph, producing less contigouos, but more detailed assembly."/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	78 <param argument="--scaffold" type="boolean" truevalue="--scaffold" falsevalue="" label="Enable scaffolding using graph"
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	79 help="Starting from the version 2.9 Flye does not perform scaffolding by default, which guarantees that all assembled sequences do not have any gaps" />
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	80 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="Perform metagenomic assembly"
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	81 help="It is designed for highly non-uniform coverage and is sensitive to underrepresented sequence at low coverage (as low as 2x).
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	82 In some examples of simple metagenomes, we observed that the normal mode assembled more contigious bacterial
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	83 consensus sequence, while the metagenome mode was slightly more fragmented, but revealed strain mixtures"/>
6 0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	84 <conditional name="asm">
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	85 <param name="asm_select" type="select" label="Reduced contig assembly coverage" help="Typically, assemblies of large genomes at high coverage require a hundreds of RAM. For high coverage assemblies,
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	86 you can reduce memory usage by using only a subset of longest reads for initial contig extension stage (usually, the memory bottleneck)">
6 0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	87 <option value="true">Enable reduced coverage for initial disjointing assembly</option>
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	88 <option value="false" selected="true">Disable reduced coverage for initial disjointing assembly</option>
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	89 </param>
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	90 <when value="true">
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	91 <param argument="--asm-coverage" type="integer" min="0" value="30"
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	92 label="Reduced coverage for initial disjointing assembly"
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	93 help="This parameter specifies the target coverage of the longest reads. For a typical assembly, 30x is enough to produce good
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	94 initial contigs. Regardless of this parameter, all reads will be used at the later pipeline stages."/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	95 <param argument="--genome-size" type="text" optional="true" label="Estimated genome size"
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	96 help="For example, 5m or 2.6g. No longer required as input. However, it must be used in conjunction with --asm-coverage option.">
6 0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	97 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	98 </param>
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	99 </when>
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	100 <when value="false" />
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	101 </conditional>
10 cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	102 <param argument="--no-alt-contigs" type="boolean" truevalue="--no-alt-contigs" falsevalue="" checked="false" label="Remove all non-primary contigs from the assembly"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	103 <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	104 </inputs>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	105 <outputs>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	106 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	107 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	108 <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	109 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	110 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	111 <filter>generate_log</filter>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	112 </data>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	113 </outputs>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	114 <tests>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	115 <!--Test 01: pacbio-raw-->
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	116 <test expect_num_outputs="5">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	117 <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	118 <param name="mode" value="--pacbio-raw"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	119 <param name="iterations" value="0"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	120 <param name="generate_log" value="true"/>
2 156e0da5b917 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit a926a92aed3e22b14fb88af204c8450987c59743 bgruening parents: 1 diff changeset	121 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
3 1ce9b1d72ec3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 9de56f311ae694ec8c636b24be7815f92521ca96 bgruening parents: 2 diff changeset	122 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
1ce9b1d72ec3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 9de56f311ae694ec8c636b24be7815f92521ca96 bgruening parents: 2 diff changeset	123 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
4 3ee0ef312022 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6" bgruening parents: 3 diff changeset	124 <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	125 <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	126 </test>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	127 <!--Test 02: nano raw-->
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	128 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	129 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	130 <param name="mode" value="--nano-raw"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	131 <param name="iterations" value="0"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	132 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	133 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	134 <has_size value="95" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	135 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	136 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	137 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	138 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	139 <has_size value="803" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	140 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	141 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	142 <output name="assembly_gfa" ftype="txt">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	143 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	144 <has_size value="35047" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	145 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	146 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	147 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	148 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	149 <has_size value="35573" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	150 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	151 </output>
4 3ee0ef312022 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6" bgruening parents: 3 diff changeset	152 </test>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	153 <!--Test 03: reduce coverage-->
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	154 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	155 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	156 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	157 <param name="mode" value="--nano-raw"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	158 </conditional>
6 0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	159 <conditional name="asm">
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	160 <param name="asm_select" value="true" />
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	161 <param name="asm" value="30"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	162 <param name="genome_size" value="3980000"/>
6 0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48" bgruening parents: 5 diff changeset	163 </conditional>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	164 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	165 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	166 <has_size value="286" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	167 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	168 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	169 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	170 <assert_contents>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	171 <has_size value="1840" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	172 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	173 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	174 <output name="assembly_gfa" ftype="txt">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	175 <assert_contents>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	176 <has_size value="420752" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	177 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	178 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	179 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	180 <assert_contents>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	181 <has_size value="427580" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	182 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	183 </output>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	184 </test>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	185 <!--Test 04: metagenomic mode-->
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	186 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	187 <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	188 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	189 <param name="mode" value="--pacbio-raw"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	190 </conditional>
4 3ee0ef312022 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6" bgruening parents: 3 diff changeset	191 <param name="meta" value="true"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	192 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	193 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	194 <has_size value="95" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	195 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	196 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	197 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	198 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	199 <has_size value="367" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	200 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	201 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	202 <output name="assembly_gfa" ftype="txt">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	203 <assert_contents>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	204 <has_size value="418729" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	205 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	206 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	207 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	208 <assert_contents>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	209 <has_size value="425667" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	210 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	211 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	212 </test>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	213 <!--Test 05: nanopore HQ mode-->
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	214 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	215 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	216 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	217 <param name="mode" value="--nano-hq"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	218 </conditional>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	219 <param name="min_overlap" value="1000"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	220 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	221 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	222 <has_size value="286" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	223 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	224 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	225 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	226 <assert_contents>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	227 <has_size value="1248" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	228 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	229 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	230 <output name="assembly_gfa" ftype="txt">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	231 <assert_contents>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	232 <has_size value="419414" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	233 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	234 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	235 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	236 <assert_contents>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	237 <has_size value="426277" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	238 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	239 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	240 </test>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	241 <!--Test 06: hifi error option-->
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	242 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	243 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	244 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	245 <param name="mode" value="--pacbio-hifi"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	246 <param name="hifi_error" value="0.21"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	247 </conditional>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	248 <param name="min_overlap" value="1000"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	249 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	250 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	251 <has_size value="286" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	252 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	253 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	254 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	255 <assert_contents>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	256 <has_size value="1500" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	257 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	258 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	259 <output name="assembly_gfa" ftype="txt">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	260 <assert_contents>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	261 <has_size value="418422" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	262 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	263 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	264 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	265 <assert_contents>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	266 <has_size value="425147" delta="200"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	267 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	268 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	269 </test>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	270 <!--Test 07: keep haplotypes-->
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	271 <test expect_num_outputs="4">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	272 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	273 <conditional name="mode_conditional">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	274 <param name="mode" value="--pacbio-corr"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	275 <param name="hifi_error" value="0.21"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	276 </conditional>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	277 <param name="min_overlap" value="1000"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	278 <param name="keep-haplotypes" value="true"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	279 <output name="assembly_info" ftype="tabular">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	280 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	281 <has_size value="286" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	282 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	283 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	284 <output name="assembly_graph" ftype="graph_dot">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	285 <assert_contents>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	286 <has_size value="1273" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	287 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	288 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	289 <output name="assembly_gfa" ftype="txt">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	290 <assert_contents>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	291 <has_size value="418511" delta="100"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	292 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	293 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	294 <output name="consensus" ftype="fasta">
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	295 <assert_contents>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	296 <has_size value="425267" delta="100"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	297 </assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	298 </output>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	299 </test>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	300 <!--Test 08: scaffolding mode-->
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	301 <test expect_num_outputs="4">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	302 <param name="inputs" ftype="fastq.gz" value="ecoli_hifi_01.fastq.gz,ecoli_hifi_02.fastq.gz,ecoli_hifi_03.fastq.gz,ecoli_hifi_04.fastq.gz,ecoli_hifi_05.fastq.gz,ecoli_hifi_06.fastq.gz,ecoli_hifi_07.fastq.gz,ecoli_hifi_08.fastq.gz,ecoli_hifi_09.fastq.gz"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	303 <param name="mode" value="--nano-hq"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	304 <param name="min_overlap" value="1000"/>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	305 <param name="scaffold" value="true"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	306 <output name="assembly_info" ftype="tabular">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	307 <assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	308 <has_size value="286" delta="100"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	309 </assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	310 </output>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	311 <output name="assembly_graph" ftype="graph_dot">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	312 <assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	313 <has_size value="1248" delta="100"/>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	314 </assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	315 </output>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	316 <output name="assembly_gfa" ftype="txt">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	317 <assert_contents>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	318 <has_size value="419414" delta="1000"/>
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	319 </assert_contents>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	320 </output>
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	321 <output name="consensus" ftype="fasta">
276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	322 <assert_contents>
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	323 <has_size value="426277" delta="1000"/>
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	324 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	325 </output>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	326 </test>
10 cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	327 <!--Test 09: test not-alt-contigs parameter w-->
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	328 <test expect_num_outputs="4">
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	329 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	330 <param name="mode" value="--nano-raw"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	331 <param name="iterations" value="0"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	332 <param name="no_alt_contigs" value="true"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	333 <output name="assembly_info" ftype="tabular">
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	334 <assert_contents>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	335 <has_size value="151" delta="100"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	336 </assert_contents>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	337 </output>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	338 <output name="assembly_graph" ftype="graph_dot">
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	339 <assert_contents>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	340 <has_size value="217" delta="100"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	341 </assert_contents>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	342 </output>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	343 <output name="assembly_gfa" ftype="txt">
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	344 <assert_contents>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	345 <has_size value="5110" delta="100"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	346 </assert_contents>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	347 </output>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	348 <output name="consensus" ftype="fasta">
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	349 <assert_contents>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	350 <has_size value="5123" delta="100"/>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	351 </assert_contents>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	352 </output>
cb8dfd28c16f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193 bgruening parents: 9 diff changeset	353 </test>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	354 </tests>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	355 <help><![CDATA[
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	356
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	357 Purpose
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	358
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	359 Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	360 It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	361 a complete pipeline: it takes raw PacBio/ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	362 assembly.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	363
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	364 ----
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	365
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	366 Quick usage
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	367
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	368 Input reads can be in FASTA or FASTQ format, uncompressed or compressed with gz. Currently, PacBio (raw, corrected, HiFi) and ONT reads
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	369 (raw, corrected) are supported. Expected error rates are <30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye was primarily
9 276f5d8712d5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3" bgruening parents: 8 diff changeset	370 developed to run on raw reads. You may specify multiple files with reads (separated by spaces). Mixing different read types is not yet supported. The --meta o
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	371 ption enables the mode for metagenome/uneven coverage assembly.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	372
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	373 Genome size estimate is no longer a required option. You need to provide an estimate if using --asm-coverage option.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	374
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	375 To reduce memory consumption for large genome assemblies, you can use a subset of the longest reads for initial disjointig assembly by
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	376 specifying --asm-coverage and --genome-size options. Typically, 40x coverage is enough to produce good disjointigs.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	377
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	378 ----
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	379
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	380 Outputs
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	381
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	382 The main output files are:
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	383
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	384 * Final assembly: contains contigs and possibly scaffolds (see below).
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	385 * Final repeat graph: note that the edge sequences might be different (shorter) than contig sequences, because contigs might include multiple graph edges.
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	386 * Extra information about contigs (such as length or coverage).
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	387
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	388 Each contig is formed by a single unique graph edge. If possible, unique contigs are extended with the sequence from flanking unresolved repeats on the graph. Thus,
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	389 a contig fully contains the corresponding graph edge (with the same id), but might be longer then this edge. This is somewhat similar to unitig-contig relation in
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	390 OLC assemblers. In a rare case when a repetitive graph edge is not covered by the set of "extended" contigs, it will be also output in the assembly file.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	391
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	392 Sometimes it is possible to further order contigs into scaffolds based on the repeat graph structure. These ordered contigs will be output as a part of scaffold in
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	393 the assembly file (with a scaffold prefix). Since it is hard to give a reliable estimate of the gap size, those gaps are represented with the default 100 Ns.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	394 assembly_info.txt file (below) contains additional information about how scaffolds were formed.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	395
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	396 Extra information about contigs/scaffolds is output into the assembly_info.txt file. It is a tab-delimited table with the columns as follows:
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	397
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	398 * Contig/scaffold id
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	399 * Length
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	400 * Coverage
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	401 * Is circular, (Y)es or (N)o
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	402 * Is repetitive, (Y)es or (N)o
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	403 * Multiplicity (based on coverage)
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	404 * Alternative group
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	405 * Graph path (graph path corresponding to this contig/scaffold).
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	406
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	407 Scaffold gaps are marked with `??` symbols, and `*` symbol denotes a terminal graph node. Alternative contigs (representing alternative haplotypes) will have the same alt.
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	408 group ID. Primary contigs are marked by `*`.
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	409
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	410 ----
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	411
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	412 Algorithm Description
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	413
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	414 This is a brief description of the Flye algorithm. Please refer to the manuscript for more detailed information. The draft contig extension is organized as follows:
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	415
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	416 * K-mer counting / erroneous k-mer pre-filtering
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	417 * Solid k-mer selection (k-mers with sufficient frequency, which are unlikely to be erroneous)
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	418 * Contig extension. The algorithm starts from a single read and extends it with a next overlapping read (overlaps are dynamically detected using the selected solid k-mers).
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	419
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	420 Note that we do not attempt to resolve repeats at this stage, thus the reconstructed contigs might contain misassemblies. Flye then aligns the reads on these draft
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	421 contigs using minimap2 and calls a consensus. Afterwards, Flye performs repeat analysis as follows:
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	422
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	423 * Repeat graph is constructed from the (possibly misassembled) contigs
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	424 * In this graph all repeats longer than minimum overlap are collapsed
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	425 * The algorithm resolves repeats using the read information and graph structure
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	426 * The unbranching paths in the graph are output as contigs
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	427
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	428 If enabled, after resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	429 Finally, Flye performs polishing of the resulting assembly to correct the remaining errors:
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	430
11 291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	431 * Alignment of all reads to the current assembly using minimap2
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	432 * Partition the alignment into mini-alignments (bubbles)
291923e6f276 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit acf41fab409bef4882d5d12cbf991452b408076e bgruening parents: 10 diff changeset	433 * Error correction of each bubble using a maximum likelihood approach
8 e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	434
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	435 The polishing steps could be repeated, which might slightly increase quality for some datasets.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	436
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	437
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48" bgruening parents: 7 diff changeset	438 ]]></help>
0 d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	439 <expand macro="citations" />
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1 bgruening parents: diff changeset	440 </tool>

Mercurial > repos > bgruening > flye

annotate flye.xml @ 11:291923e6f276 draft default tip