annotate miniasm.xml @ 5:80d1250bd5fd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 8b64dd57d6b732e97693d068ebf9d3fb9f25fc8c"
author iuc
date Sat, 23 Oct 2021 21:50:09 +0000
parents a7b889b90140
children b799a615995d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
80d1250bd5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 8b64dd57d6b732e97693d068ebf9d3fb9f25fc8c"
iuc
parents: 4
diff changeset
1 <tool id="miniasm" name="miniasm" version="@TOOL_VERSION@+galaxy1" profile="20.05">
0
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
2 <description>Ultrafast de novo assembly for long noisy reads </description>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
3 <macros>
4
a7b889b90140 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 1791aec80ff00e41618b5d96947498e334bfebc9"
iuc
parents: 3
diff changeset
4 <token name="@TOOL_VERSION@">0.3_r179</token>
0
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
5 </macros>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
6 <requirements>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">miniasm</requirement>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
8 </requirements>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
9 <version_command>miniasm -V</version_command>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
11 miniasm
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
12 -f '$readFile'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
13 -m '$preselection.minMatch'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
14 -i '$preselection.minIden'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
15 -s '$preselection.minSpan'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
16 -c '$preselection.minCov'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
17 -o '$overlapping.minOvlp'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
18 -h '$overlapping.maxHang'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
19 -I '$overlapping.intThres'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
20 -g '$graph.maxGapDiff'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
21 -d '$graph.maxBubDist'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
22 -e '$graph.minUtgSize'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
23 -n '$graph.nRounds'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
24 -F '$graph.finalDropRatio'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
25 '$paf' > '$gfa'
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
26 ]]></command>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
27 <inputs>
3
73a3846701e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 5b819c9a19a38ebdd60bcd0ea3f530bf60a688bb"
iuc
parents: 2
diff changeset
28 <param name="readFile" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Sequence Reads" />
5
80d1250bd5fd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 8b64dd57d6b732e97693d068ebf9d3fb9f25fc8c"
iuc
parents: 4
diff changeset
29 <param name="paf" type="data" format="paf" label="PAF file" help="Pairwise mapping format" />
0
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
30 <section name="preselection" title="Preselection options">
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
31 <param argument="-m" name="minMatch" type="integer" value="100" label="Drop mappings having less than this number of matching bases"
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
32 help="column 10 in PAF"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
33 <param argument="-i" name="minIden" type="float" value="0.05" label="During read filtering, ignore mappings with col10/col11 below this value"
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
34 help="Ignored mappings are still used for read overlaps" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
35 <param argument="-s" name="minSpan" type="integer" value="1000" label="Drop mappings shorter than this number bp"
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
36 help="This option also affects the second round of read filtering and minimal overlap length"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
37 <param argument="-c" name="minCov" type="integer" value="3" label="Minimal coverage by other reads"
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
38 help="In the first round of filtering, miniasm finds the longest region covered by this number or more reads. In the second round, it in addition requires each remaining base to be covered by this many bases at least minSpan/2 from the ends of other reads" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
39 </section>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
40 <section name="overlapping" title="Overlapping options">
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
41 <param argument="-o" name="minOvlp" type="integer" value="1000" label="Minimal overlap length [same as minSpan]" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
42 <param argument="-h" name="maxHang" type="integer" value="1000" label="Maximum overhang length"
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
43 help="An overhang is an unmapped region that should be mapped given a true overlap or true containment. If the overhang is too long, the mapping is considered an internal match and will be ignored" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
44 <param argument="-I" name="intThres" type="float" value="0.08" label="Minimal ratio of mapping length to mapping+overhang length for a mapping considered a containment or an overlap"
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
45 help="This option has a similar role to MaxHang, except that it controls the ratio, not length" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
46 </section>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
47 <section name="graph" title="Graph layout options">
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
48 <param argument="-g" name="maxGapDiff" type="integer" value="1000" label="Maximal gap differences between two reads in a mapping"
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
49 help="This parameter is only used for transitive reduction" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
50 <param argument="-d" name="maxBubDist" type="integer" value="50000" label="Maximal probing distance for bubble popping"
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
51 help="Bubbles longer than this value will not be popped" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
52 <param argument="-e" name="minUtgSize" type="integer" value="4" label="A unitig is considered small if it is composed of less than this many reads"
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
53 help="Miniasm may try to remove small unitigs at various steps"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
54 <param argument="-n" name="nRounds" type="integer" value="3" label="Rounds of short overlap removal" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
55 <param argument="-F" name="finalDropRatio" type="float" value="0.8" label="Overlap drop ratio threshold after short unitig removal" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
56 </section>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
57 </inputs>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
58 <outputs>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
59 <data name="gfa" format="tabular" label="${tool.name} on ${on_string}: Assembly Graph" />
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
60 </outputs>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
61 <tests>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
62 <test>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
63 <param name="readFile" value="mini_reads.fq"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
64 <param name="paf" value="mini_reads.paf.gz"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
65 <output name="gfa" file="mini_reads.gfa"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
66 </test>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
67 <test>
3
73a3846701e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 5b819c9a19a38ebdd60bcd0ea3f530bf60a688bb"
iuc
parents: 2
diff changeset
68 <param name="readFile" value="mini_reads.fq.gz"/>
0
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
69 <param name="minMatch" value="99"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
70 <param name="minIden" value="0.04"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
71 <param name="minSpan" value="999"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
72 <param name="minCov" value="2"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
73 <param name="minOvlp" value="999"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
74 <param name="maxHang" value="999"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
75 <param name="intThres" value="0.7"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
76 <param name="maxGapDiff" value="999"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
77 <param name="maxBubDist" value="45000"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
78 <param name="minUtgSize" value="3"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
79 <param name="nRounds" value="2"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
80 <param name="finalDropRatio" value="0.7"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
81 <param name="paf" value="mini_reads.paf.gz"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
82 <output name="gfa" file="reads_advanced.gfa"/>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
83 </test>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
84 </tests>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
85 <help><![CDATA[
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
86 Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
87 (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers,
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
88 miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
89 sequences. Thus the per-base error rate is similar to the raw input reads.
2
8dee0218ac7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit d225098ffed70a721aa688a57b7fe42815a9f042"
iuc
parents: 1
diff changeset
90
8dee0218ac7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit d225098ffed70a721aa688a57b7fe42815a9f042"
iuc
parents: 1
diff changeset
91 NOTE: This tool may take a long time depending on the size and characteristics of your dataset.
0
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
92 ]]></help>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
93 <citations>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
94 <citation type="doi">10.1093/bioinformatics/btw152</citation>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
95 </citations>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
96 </tool>
8b6d0d85252b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm commit 4e244b45154a712c786f6bca774e0b25676f4642
iuc
parents:
diff changeset
97