Mercurial > repos > bgruening > flye

annotate flye.xml @ 10:7066276883d6 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 3507b06e5d0149d514ede3d1a56c082e89f14f89
author bgruening
date Mon, 26 Aug 2024 13:54:16 +0000
parents 5f2671cec451
children 6e5b72b4e1fb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
1 <tool id="flye" name="Flye" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
2 <description>de novo assembler for single molecule sequencing reads</description>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
3 <macros>
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
4 <import>macros.xml</import>
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
5 </macros>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
6 <expand macro="edam_ontology"/>
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
7 <expand macro="xrefs"/>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
8 <expand macro="requirements" />
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
9 <version_command>flye --version</version_command>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
11 #for $counter, $input in enumerate($inputs):
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
12 #if $input.is_of_type('fastqsanger', 'fastq'):
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
13 #set $ext = 'fastq'
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
14 #elif $input.is_of_type('fastqsanger.gz', 'fastq.gz'):
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
15 #set $ext = 'fastq.gz'
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
16 #elif $input.is_of_type('fasta.gz'):
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
17 #set $ext = 'fasta.gz'
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
18 #elif $input.is_of_type('fasta'):
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
19 #set $ext = 'fasta'
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
20 #end if
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
21 ln -sf '$input' ./input_${counter}.${ext} &&
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
22 #end for
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
23 flye
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
24 $mode_conditional.mode
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
25 #for $counter, $input in enumerate($inputs):
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
26 ./input_${counter}.$ext
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
27 #end for
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
28 -o out_dir
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
29 -t \${GALAXY_SLOTS:-4}
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
30 -i $iterations
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
31 #if $mode_conditional.mode == '--pacbio-hifi' and $mode_conditional.hifi_error:
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
32 --hifi-error $mode_conditional.hifi_error
1
6e7b5193ec26 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 6cd5f829f985631f0e8360d66a73206389101171
bgruening
parents: 0
diff changeset
33 #end if
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
34 #if $min_overlap:
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
35 -m $min_overlap
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
36 #end if
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
37 #if $asm.asm_select == 'true':
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
38 --asm-coverage $asm.asm_coverage
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
39 -g '${asm.genome_size}'
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
40 #end if
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
41 $meta
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
42 $scaffold
9
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
43 $no_alt_contigs
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
44 ]]></command>
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
45 <inputs>
1
6e7b5193ec26 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 6cd5f829f985631f0e8360d66a73206389101171
bgruening
parents: 0
diff changeset
46 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
47 <conditional name="mode_conditional">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
48 <param name="mode" type="select" label="Mode">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
49 <option value="--nano-raw">Nanopore raw (--nano-raw)</option>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
50 <option value="--nano-corr">Nanopore corrected (--nano-corr)</option>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
51 <option value="--nano-hq">Nanopore HQ (--nano-hq)</option>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
52 <option value="--pacbio-raw">PacBio raw (--pacbio-raw)</option>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
53 <option value="--pacbio-corr">PacBio corrected (--pacbio-corr)</option>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
54 <option value="--pacbio-hifi">PacBio HiFi (--pacbio-hifi)</option>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
55 </param>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
56 <when value="--nano-raw"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
57 <when value="--nano-corr"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
58 <when value="--nano-hq"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
59 <when value="--pacbio-raw"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
60 <when value="--pacbio-corr"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
61 <when value="--pacbio-hifi">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
62 <param argument="--hifi-error" type="float" min="0" max="1" optional="true" label="Expected HiFi reads error rate" help="Default: 0.01"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
63 </when>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
64 </conditional>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
65 <param argument="--iterations" type="integer" value="1" label="Number of polishing iterations"
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
66 help="Polishing is performed as the final assembly stage. By default, Flye runs one polishing iteration. Additional iterations
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
67 might correct a small number of extra errors (due to improvements on how reads may align to the corrected assembly). If the
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
68 parameter is set to 0, the polishing is not performed"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
69 <param argument="--min-overlap" type="integer" min="1000" max="10000" optional="true" label="Minimum overlap between reads"
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
70 help="This sets a minimum overlap length for two reads to be considered overlapping. By default it is chosen
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
71 automatically based on the read length distribution (reads N90) and does not require manual setting. Typical
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
72 value is 3k-5k (and down to 1k for datasets with shorter read length). Intuitively, we want to set this
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
73 parameter as high as possible, so the repeat graph is less tangled. However, higher values might lead to assembly gaps.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
74 In some rare cases it makes sense to manually increase minimum overlap for assemblies of big genomes with long reads and high coverage." />
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
75 <param argument="--keep-haplotypes" type="boolean" truevalue="--keep-haplotypes" falsevalue="" checked="False" label="Keep haplotypes"
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
76 help="By default, Flye collapses graph structures caused by alternative haplotypes (bubbles, superbubbles, roundabouts) to produce longer
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
77 consensus contigs. This option retains the alternative paths on the graph, producing less contigouos, but more detailed assembly."/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
78 <param argument="--scaffold" type="boolean" truevalue="--scaffold" falsevalue="" label="Enable scaffolding using graph"
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
79 help="Starting from the version 2.9 Flye does not perform scaffolding by default, which guarantees that all assembled sequences do not have any gaps" />
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
80 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="Perform metagenomic assembly"
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
81 help="It is designed for highly non-uniform coverage and is sensitive to underrepresented sequence at low coverage (as low as 2x).
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
82 In some examples of simple metagenomes, we observed that the normal mode assembled more contigious bacterial
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
83 consensus sequence, while the metagenome mode was slightly more fragmented, but revealed strain mixtures"/>
6
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
84 <conditional name="asm">
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
85 <param name="asm_select" type="select" label="Reduced contig assembly coverage" help="Typically, assemblies of large genomes at high coverage require a hundreds of RAM. For high coverage assemblies,
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
86 you can reduce memory usage by using only a subset of longest reads for initial contig extension stage (usually, the memory bottleneck)">
6
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
87 <option value="true">Enable reduced coverage for initial disjointing assembly</option>
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
88 <option value="false" selected="true">Disable reduced coverage for initial disjointing assembly</option>
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
89 </param>
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
90 <when value="true">
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
91 <param argument="--asm-coverage" type="integer" min="0" value="30"
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
92 label="Reduced coverage for initial disjointing assembly"
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
93 help="This parameter specifies the target coverage of the longest reads. For a typical assembly, 30x is enough to produce good
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
94 initial contigs. Regardless of this parameter, all reads will be used at the later pipeline stages."/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
95 <param argument="--genome-size" type="text" optional="true" label="Estimated genome size"
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
96 help="For example, 5m or 2.6g. No longer required as input. However, it must be used in conjunction with --asm-coverage option.">
6
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
97 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
98 </param>
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
99 </when>
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
100 <when value="false" />
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
101 </conditional>
9
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
102 <param argument="--no-alt-contigs" type="boolean" truevalue="--no-alt-contigs" falsevalue="" checked="false" label="Remove all non-primary contigs from the assembly"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
103 <param name="generate_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a log file"/>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
104 </inputs>
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
105 <outputs>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
106 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string}: consensus"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
107 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string}: assembly graph"/>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
108 <data name="assembly_gfa" format="gfa" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string}: graphical fragment assembly"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
109 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string}: assembly info"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
110 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string}: log">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
111 <filter>generate_log</filter>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
112 </data>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
113 </outputs>
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
114 <tests>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
115 <!--Test 01: pacbio-raw-->
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
116 <test expect_num_outputs="5">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
117 <param name="inputs" ftype="fastq.gz" value="ecoli_01.fastq.gz,ecoli_02.fastq.gz,ecoli_03.fastq.gz,ecoli_04.fastq.gz,ecoli_05.fastq.gz,ecoli_06.fastq.gz,ecoli_07.fastq.gz"/>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
118 <param name="mode" value="--pacbio-raw"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
119 <param name="iterations" value="0"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
120 <param name="generate_log" value="true"/>
2
792735cc7ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit a926a92aed3e22b14fb88af204c8450987c59743
bgruening
parents: 1
diff changeset
121 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
3
c5417aa9eb4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 9de56f311ae694ec8c636b24be7815f92521ca96
bgruening
parents: 2
diff changeset
122 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
123 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="gfa" compare="diff" lines_diff="10"/>
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
124 <output name="consensus" ftype="fasta">
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
125 <assert_contents>
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
126 <has_line line=">contig_1"/>
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
127 </assert_contents>
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
128 </output>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
129 <output name="flye_log" file="result1.log" ftype="txt" compare="sim_size"/>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
130 </test>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
131 <!--Test 02: nano raw-->
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
132 <test expect_num_outputs="4">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
133 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
134 <param name="mode" value="--nano-raw"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
135 <param name="iterations" value="0"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
136 <output name="assembly_info" ftype="tabular">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
137 <assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
138 <has_size value="95" delta="100"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
139 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
140 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
141 <output name="assembly_graph" ftype="graph_dot">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
142 <assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
143 <has_size value="803" delta="100"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
144 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
145 </output>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
146 <output name="assembly_gfa" ftype="gfa">
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
147 <assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
148 <has_size value="35047" delta="100"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
149 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
150 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
151 <output name="consensus" ftype="fasta">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
152 <assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
153 <has_size value="35573" delta="100"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
154 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
155 </output>
4
fed3d7b3ef6b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
bgruening
parents: 3
diff changeset
156 </test>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
157 <!--Test 03: reduce coverage-->
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
158 <test expect_num_outputs="4">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
159 <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"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
160 <conditional name="mode_conditional">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
161 <param name="mode" value="--nano-raw"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
162 </conditional>
6
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
163 <conditional name="asm">
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
164 <param name="asm_select" value="true" />
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
165 <param name="asm" value="30"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
166 <param name="genome_size" value="3980000"/>
6
d87d93f44f9e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
bgruening
parents: 5
diff changeset
167 </conditional>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
168 <output name="assembly_info" ftype="tabular">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
169 <assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
170 <has_size value="286" delta="100"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
171 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
172 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
173 <output name="assembly_graph" ftype="graph_dot">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
174 <assert_contents>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
175 <has_size value="1840" delta="100"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
176 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
177 </output>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
178 <output name="assembly_gfa" ftype="gfa">
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
179 <assert_contents>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
180 <has_size value="420752" delta="100"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
181 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
182 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
183 <output name="consensus" ftype="fasta">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
184 <assert_contents>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
185 <has_size value="427580" delta="100"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
186 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
187 </output>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
188 </test>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
189 <!--Test 04: metagenomic mode-->
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
190 <test expect_num_outputs="4">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
191 <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"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
192 <conditional name="mode_conditional">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
193 <param name="mode" value="--pacbio-raw"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
194 </conditional>
4
fed3d7b3ef6b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
bgruening
parents: 3
diff changeset
195 <param name="meta" value="true"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
196 <output name="assembly_info" ftype="tabular">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
197 <assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
198 <has_size value="95" delta="100"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
199 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
200 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
201 <output name="assembly_graph" ftype="graph_dot">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
202 <assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
203 <has_size value="367" delta="100"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
204 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
205 </output>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
206 <output name="assembly_gfa" ftype="gfa">
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
207 <assert_contents>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
208 <has_size value="418729" delta="100"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
209 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
210 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
211 <output name="consensus" ftype="fasta">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
212 <assert_contents>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
213 <has_size value="425667" delta="100"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
214 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
215 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
216 </test>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
217 <!--Test 05: nanopore HQ mode-->
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
218 <test expect_num_outputs="4">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
219 <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"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
220 <conditional name="mode_conditional">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
221 <param name="mode" value="--nano-hq"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
222 </conditional>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
223 <param name="min_overlap" value="1000"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
224 <output name="assembly_info" ftype="tabular">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
225 <assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
226 <has_size value="286" delta="100"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
227 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
228 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
229 <output name="assembly_graph" ftype="graph_dot">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
230 <assert_contents>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
231 <has_size value="1248" delta="100"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
232 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
233 </output>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
234 <output name="assembly_gfa" ftype="gfa">
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
235 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
236 <has_size value="419414" delta="1000"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
237 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
238 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
239 <output name="consensus" ftype="fasta">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
240 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
241 <has_size value="426277" delta="1000"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
242 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
243 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
244 </test>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
245 <!--Test 06: hifi error option-->
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
246 <test expect_num_outputs="4">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
247 <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"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
248 <conditional name="mode_conditional">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
249 <param name="mode" value="--pacbio-hifi"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
250 <param name="hifi_error" value="0.21"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
251 </conditional>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
252 <param name="min_overlap" value="1000"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
253 <output name="assembly_info" ftype="tabular">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
254 <assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
255 <has_size value="286" delta="100"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
256 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
257 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
258 <output name="assembly_graph" ftype="graph_dot">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
259 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
260 <has_size value="1248" delta="500"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
261 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
262 </output>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
263 <output name="assembly_gfa" ftype="gfa">
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
264 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
265 <has_size value="420254" delta="2000"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
266 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
267 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
268 <output name="consensus" ftype="fasta">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
269 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
270 <has_size value="427131" delta="2000"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
271 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
272 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
273 </test>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
274 <!--Test 07: keep haplotypes-->
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
275 <test expect_num_outputs="4">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
276 <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"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
277 <conditional name="mode_conditional">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
278 <param name="mode" value="--pacbio-corr"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
279 <param name="hifi_error" value="0.21"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
280 </conditional>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
281 <param name="min_overlap" value="1000"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
282 <param name="keep-haplotypes" value="true"/>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
283 <output name="assembly_info" ftype="tabular">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
284 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
285 <has_size value="286" delta="200"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
286 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
287 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
288 <output name="assembly_graph" ftype="graph_dot">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
289 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
290 <has_size value="1273" delta="500"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
291 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
292 </output>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
293 <output name="assembly_gfa" ftype="gfa">
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
294 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
295 <has_size value="420254" delta="3000"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
296 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
297 </output>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
298 <output name="consensus" ftype="fasta">
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
299 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
300 <has_size value="427131" delta="3000"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
301 </assert_contents>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
302 </output>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
303 </test>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
304 <!--Test 08: scaffolding mode-->
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
305 <test expect_num_outputs="4">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
306 <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"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
307 <param name="mode" value="--nano-hq"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
308 <param name="min_overlap" value="1000"/>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
309 <param name="scaffold" value="true"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
310 <output name="assembly_info" ftype="tabular">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
311 <assert_contents>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
312 <has_size value="286" delta="100"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
313 </assert_contents>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
314 </output>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
315 <output name="assembly_graph" ftype="graph_dot">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
316 <assert_contents>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
317 <has_size value="1248" delta="100"/>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
318 </assert_contents>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
319 </output>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
320 <output name="assembly_gfa" ftype="gfa">
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
321 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
322 <has_size value="419414" delta="2000"/>
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
323 </assert_contents>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
324 </output>
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
325 <output name="consensus" ftype="fasta">
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
326 <assert_contents>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
327 <has_size value="426277" delta="2000"/>
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
328 </assert_contents>
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
329 </output>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
330 </test>
9
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
331 <!--Test 09: test not-alt-contigs parameter w-->
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
332 <test expect_num_outputs="4">
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
333 <param name="inputs" ftype="fasta.gz" value="nanopore.fasta.gz"/>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
334 <param name="mode" value="--nano-raw"/>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
335 <param name="iterations" value="0"/>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
336 <param name="no_alt_contigs" value="true"/>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
337 <output name="assembly_info" ftype="tabular">
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
338 <assert_contents>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
339 <has_size value="151" delta="100"/>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
340 </assert_contents>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
341 </output>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
342 <output name="assembly_graph" ftype="graph_dot">
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
343 <assert_contents>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
344 <has_size value="217" delta="100"/>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
345 </assert_contents>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
346 </output>
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
347 <output name="assembly_gfa" ftype="gfa">
9
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
348 <assert_contents>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
349 <has_size value="5110" delta="100"/>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
350 </assert_contents>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
351 </output>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
352 <output name="consensus" ftype="fasta">
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
353 <assert_contents>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
354 <has_size value="5123" delta="100"/>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
355 </assert_contents>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
356 </output>
5f2671cec451 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit c15c09d6f7f59753d2980da774ffeced15836193
bgruening
parents: 8
diff changeset
357 </test>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
358 </tests>
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
359 <help><![CDATA[
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
360
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
361 **Purpose**
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
362
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
363 Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
364 It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
365 a complete pipeline: it takes raw PacBio/ONT reads as input and outputs polished contigs. Flye also has a special mode for metagenome
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
366 assembly.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
367
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
368 ----
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
369
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
370 **Quick usage**
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
371
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
372 Input reads can be in FASTA or FASTQ format, uncompressed or compressed with gz. Currently, PacBio (raw, corrected, HiFi) and ONT reads
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
373 (raw, corrected) are supported. Expected error rates are <30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye was primarily
8
2522110f3cb4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7c956f5b897dc366b2e5b7e37a2fea4b51a814f3"
bgruening
parents: 7
diff changeset
374 developed to run on raw reads. You may specify multiple files with reads (separated by spaces). Mixing different read types is not yet supported. The *--meta* o
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
375 ption enables the mode for metagenome/uneven coverage assembly.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
376
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
377 Genome size estimate is no longer a required option. You need to provide an estimate if using *--asm-coverage* option.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
378
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
379 To reduce memory consumption for large genome assemblies, you can use a subset of the longest reads for initial disjointig assembly by
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
380 specifying *--asm-coverage* and *--genome-size* options. Typically, 40x coverage is enough to produce good disjointigs.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
381
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
382 ----
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
383
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
384 **Outputs**
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
385
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
386 The main output files are:
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
387
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
388 * Final assembly: contains contigs and possibly scaffolds (see below).
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
389 * Final repeat graph: note that the edge sequences might be different (shorter) than contig sequences, because contigs might include multiple graph edges.
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
390 * Extra information about contigs (such as length or coverage).
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
391
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
392 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,
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
393 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
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
394 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.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
395
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
396 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
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
397 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.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
398 assembly_info.txt file (below) contains additional information about how scaffolds were formed.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
399
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
400 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
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
401
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
402 * Contig/scaffold id
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
403 * Length
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
404 * Coverage
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
405 * Is circular, (Y)es or (N)o
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
406 * Is repetitive, (Y)es or (N)o
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
407 * Multiplicity (based on coverage)
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
408 * Alternative group
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
409 * Graph path (graph path corresponding to this contig/scaffold).
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
410
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
411 Scaffold gaps are marked with `??` symbols, and `*` symbol denotes a terminal graph node. Alternative contigs (representing alternative haplotypes) will have the same alt.
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
412 group ID. Primary contigs are marked by `*`.
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
413
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
414 ----
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
415
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
416 **Algorithm Description**
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
417
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
418 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:
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
419
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
420 * K-mer counting / erroneous k-mer pre-filtering
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
421 * Solid k-mer selection (k-mers with sufficient frequency, which are unlikely to be erroneous)
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
422 * 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).
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
423
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
424 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
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
425 contigs using minimap2 and calls a consensus. Afterwards, Flye performs repeat analysis as follows:
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
426
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
427 * Repeat graph is constructed from the (possibly misassembled) contigs
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
428 * In this graph all repeats longer than minimum overlap are collapsed
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
429 * The algorithm resolves repeats using the read information and graph structure
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
430 * The unbranching paths in the graph are output as contigs
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
431
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
432 If enabled, after resolving bridged repeats, Trestle module attempts to resolve simple unbridged repeats (of multiplicity 2) using the heterogeneities between repeat copies.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
433 Finally, Flye performs polishing of the resulting assembly to correct the remaining errors:
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
434
10
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
435 * Alignment of all reads to the current assembly using minimap2
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
436 * Partition the alignment into mini-alignments (bubbles)
7066276883d6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 3507b06e5d0149d514ede3d1a56c082e89f14f89
bgruening
parents: 9
diff changeset
437 * Error correction of each bubble using a maximum likelihood approach
7
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
438
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
439 The polishing steps could be repeated, which might slightly increase quality for some datasets.
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
440
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
441
28898f6f2352 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 7bec5df9cb30dd196ae99565d77547e12d05fa48"
bgruening
parents: 6
diff changeset
442 ]]></help>
0
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
443 <expand macro="citations" />
5a6e12e067a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
diff changeset
444 </tool>