Mercurial > repos > bgruening > flye

annotate flye.xml @ 8:e27815e82dd4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
author bgruening
date Wed, 30 Jun 2021 20:02:51 +0000
parents 8d4f03b5fe9d
children 276f5d8712d5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
6 <expand macro="requirements" />
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
7 <expand macro="edam_ontology"/>
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
8 <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
9 <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
10 #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
11 #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
12 #set $ext = 'fastq'
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
13 #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
14 #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
15 #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
16 #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
17 #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
18 #set $ext = 'fasta'
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
19 #end if
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
20 ln -s '$input' ./input_${counter}.${ext} &&
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
21 #end for
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
22 flye
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
23 $mode
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
24 #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
25 ./input_${counter}.$ext
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
26 #end for
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
27 -o out_dir
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
28 -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
29 -i $iterations
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
30 #if $hifi_error:
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
31 --hifi-error $hifi_error
1
cd256484eb1a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 6cd5f829f985631f0e8360d66a73206389101171
bgruening
parents: 0
diff changeset
32 #end if
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
33 #if $min_overlap:
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
34 -m $min_overlap
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
35 #end if
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
36 #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
37 --asm-coverage $asm.asm_coverage
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
38 -g '${asm.genome_size}'
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
39 #end if
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
40 $plasmids
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
41 $meta
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
42 $trestle
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
43 ]]></command>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
44 <inputs>
1
cd256484eb1a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 6cd5f829f985631f0e8360d66a73206389101171
bgruening
parents: 0
diff changeset
45 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
46 <param name="mode" type="select" label="Mode">
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
47 <option value="--nano-raw">Nanopore raw</option>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
48 <option value="--nano-corr">Nanopore corrected</option>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
49 <option value="--pacbio-hifi">PacBio HiFi</option>
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
50 <option value="--pacbio-raw">PacBio raw</option>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
51 <option value="--pacbio-corr">PacBio corrected</option>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
52 <option value="--subassemblies">High-quality contig-like input</option>
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
53 </param>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
54 <param argument="--iterations" type="integer" value="0" label="Number of polishing iterations"
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
55 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
56 might correct a small number of extra errors (due to improvements on how reads may align to the corrected assembly). If the
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
57 parameter is set to 0, the polishing is not performed."/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
58 <param argument="--min-overlap" type="integer" optional="true" label="Minimum overlap between reads"
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
59 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
60 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
61 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
62 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
63 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
64 <param argument="--hifi-error" type="float" min="0" max="1" optional="true" label="Expected HiFi reads error rate" help="Default: 0.01"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
65 <param argument="--plasmids" type="boolean" truevalue="--plasmids" falsevalue="" checked="False" label="Rescue short unassembled plasmids" />
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
66 <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
67 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
68 consensus contigs. This option retains the alternative paths on the graph, producing less contigouos, but more detailed assembly."/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
69 <param argument="--trestle" type="boolean" truevalue="--trestle" falsevalue=""
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
70 checked="False" label="Enable Trestle"
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
71 help="Trestle is an extra module that resolves simple repeats of multipicity 2 that were not bridged by reads. Depending on the datasets, it might
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
72 resolve a few extra repeats, which is helpful for small (bacterial genomes). On large genomes, the contiguity improvements are usually minimal,
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
73 but the computation might take a lot of time" />
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
74 <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
75 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
76 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
77 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
78 <conditional name="asm">
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
79 <param name="asm_select" type="select" label="Reduced contig assembly coverage">
6
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
80 <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
81 <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
82 </param>
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
83 <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
84 <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
85 label="Reduced coverage for initial disjointing assembly"
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
86 help="Typically, assemblies of large genomes at high coverage require a hundreds of RAM. For high coverage assemblies,
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
87 you can reduce memory usage by using only a subset of longest reads for initial contig extension stage (usually, the memory bottleneck).
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
88 The parameter --asm-coverage specifies the target coverage of the longest reads. For a typical assembly, 30x is enough to produce good
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
89 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
90 <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
91 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
92 <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
93 </param>
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
94 </when>
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
95 <when value="false" />
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
96 </conditional>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
97 <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
98 </inputs>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
99 <outputs>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
100 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
101 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
102 <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
103 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
104 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${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
105 <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
106 </data>
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
107 </outputs>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
108 <tests>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
109 <!--Test 01-->
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
110 <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
111 <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
112 <param name="mode" value="--pacbio-raw"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
113 <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
114 <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
115 <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
116 <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
117 <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
118 <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
119 </test>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
120 <!--Test 02-->
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
121 <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
122 <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
123 <param name="mode" value="--nano-raw"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
124 <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
125 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
126 <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
127 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
128 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
129 <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
130 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
131 <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
132 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
133 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
134 <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
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 <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
137 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
138 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
139 <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
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 <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
142 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
143 </output>
4
3ee0ef312022 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
bgruening
parents: 3
diff changeset
144 </test>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
145 <!--Test 03-->
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
146 <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
147 <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"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
148 <param name="mode" value="--pacbio-hifi"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
149 <param name="iterations" value="1"/>
6
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
150 <conditional name="asm">
0284be52bfcf "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
151 <param name="asm_select" value="true" />
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
152 <param name="asm" value="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
153 <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
154 </conditional>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
155 <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
156 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
157 <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
158 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
159 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
160 <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
161 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
162 <has_size value="2135" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
163 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
164 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
165 <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
166 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
167 <has_size value="114351" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
168 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
169 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
170 <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
171 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
172 <has_size value="116191" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
173 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
174 </output>
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
175 </test>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
176 <!--Test 04-->
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
177 <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
178 <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
179 <param name="mode" value="--pacbio-raw"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
180 <param name="iterations" value="1"/>
4
3ee0ef312022 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
bgruening
parents: 3
diff changeset
181 <param name="meta" value="true"/>
3ee0ef312022 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
bgruening
parents: 3
diff changeset
182 <param name="plasmids" value="true"/>
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
183 <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
184 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
185 <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
186 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
187 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
188 <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
189 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
190 <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
191 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
192 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
193 <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
194 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
195 <has_size value="418051" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
196 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
197 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
198 <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
199 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
200 <has_size value="425000" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
201 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
202 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
203 </test>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
204 <!--Test 05-->
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
205 <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
206 <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"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
207 <param name="mode" value="--pacbio-hifi"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
208 <param name="iterations" value="1"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
209 <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
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 <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
212 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
213 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
214 <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
215 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
216 <has_size value="2135" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
217 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
218 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
219 <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
220 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
221 <has_size value="114351" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
222 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
223 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
224 <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
225 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
226 <has_size value="116191" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
227 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
228 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
229 </test>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
230 <!--Test 06-->
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
231 <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
232 <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"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
233 <param name="mode" value="--pacbio-hifi"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
234 <param name="iterations" value="1"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
235 <param name="hifi-error" value="0.02"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
236 <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
237 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
238 <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
239 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
240 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
241 <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
242 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
243 <has_size value="2135" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
244 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
245 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
246 <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
247 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
248 <has_size value="114351" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
249 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
250 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
251 <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
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 <has_size value="116191" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
254 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
255 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
256 </test>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
257 <!--Test 07-->
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
258 <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
259 <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"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
260 <param name="mode" value="--pacbio-hifi"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
261 <param name="iterations" value="1"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
262 <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
263 <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
264 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
265 <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
266 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
267 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
268 <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
269 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
270 <has_size value="2135" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
271 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
272 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
273 <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
274 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
275 <has_size value="114351" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
276 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
277 </output>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
278 <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
279 <assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
280 <has_size value="116191" delta="100"/>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
281 </assert_contents>
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
282 </output>
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
283 </test>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
284 </tests>
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
285 <help><![CDATA[
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
286
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
287 .. class:: infomark
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
288
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
289 **Purpose**
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
290
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
291 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
292 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
293 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
294 assembly.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
295
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
296 ----
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
297
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
298 .. class:: infomark
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
299
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
300 **Quick usage**
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
301
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
302 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
303 (raw, corrected) are supported. Expected error rates are <30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye was primarily
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
304 developed to run on raw reads. Additionally, the *--subassemblies* option performs a consensus assembly of multiple sets of high-quality
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
305 contigs. You may specify multiple files with reads (separated by spaces). Mixing different read types is not yet supported. The *--meta* o
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
306 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
307
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
308 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
309
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
310 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
311 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
312
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
313 ----
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
314
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
315 .. class:: infomark
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
316
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
317 **Outputs**
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
318
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
319 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
320
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
321 ::
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
322
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
323 - Final assembly: contains contigs and possibly scaffolds (see below).
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
324 - Final repeat graph: note that the edge sequences might be different (shorter) than contig sequences, because contigs might include multiple graph edges.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
325 - Extra information about contigs (such as length or coverage).
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
326
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
327 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
328 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
329 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
330
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
331 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
332 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
333 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
334
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
335 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
336
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
337 ::
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
338
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
339 - Contig/scaffold id
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
340 - Length
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
341 - Coverage
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
342 - Is circular, (Y)es or (N)o
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
343 - Is repetitive, (Y)es or (N)o
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
344 - Multiplicity (based on coverage)
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
345 - Alternative group
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
346 - Graph path (graph path corresponding to this contig/scaffold).
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
347
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
348 Scaffold gaps are marked with ?? symbols, and * symbol denotes a terminal graph node. Alternative contigs (representing alternative haplotypes) will have the same alt.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
349 group ID. Primary contigs are marked by *.
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
350
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
351 ----
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
352
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
353 .. class:: infomark
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
354
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
355 **Algorithm Description**
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
356
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
357 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
358
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
359 ::
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
360
8
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
361 - K-mer counting / erroneous k-mer pre-filtering
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
362 - Solid k-mer selection (k-mers with sufficient frequency, which are unlikely to be erroneous)
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
363 - 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).
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 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
366 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
367
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
368 ::
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
369
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
370 - Repeat graph is constructed from the (possibly misassembled) contigs
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
371 - In this graph all repeats longer than minimum overlap are collapsed
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
372 - The algorithm resolves repeats using the read information and graph structure
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
373 - The unbranching paths in the graph are output as contigs
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 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
376 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
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 - Alignment of all reads to the current assembly using minimap2
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
381 - Partition the alignment into mini-alignments (bubbles)
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
382 - Error correction of each bubble using a maximum likelihood approach
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
383
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
384
e27815e82dd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 7
diff changeset
385 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
386
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 ]]></help>
0
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
389 <expand macro="citations" />
d9f4c141d88a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
390 </tool>