Mercurial > repos > bgruening > minipolish
comparison minipolish.xml @ 0:1f9f2edc8cf4 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/minipolish commit 2772d922443f5838d84646282be6fbfad2df1c77
author | bgruening |
---|---|
date | Wed, 19 Oct 2022 14:58:27 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:1f9f2edc8cf4 |
---|---|
1 <tool id="minipolish" name="minipolish" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01"> | |
2 <description>polishing miniasm assemblies</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <expand macro="biotools"/> | |
8 <version_command>gfastats --version</version_command> | |
9 <command detect_errors="exit_code"><![CDATA[ | |
10 #if $reads.ext.startswith("fasta") | |
11 #set ext="fasta" | |
12 #else | |
13 #set ext="fastq" | |
14 #end if | |
15 #if $reads.ext.endswith(".gz") | |
16 #set ext=ext+".gz" | |
17 #end if | |
18 ln -s '$reads' reads.$ext && | |
19 minipolish | |
20 -t \${GALAXY_SLOTS:-4} | |
21 --rounds $rounds | |
22 $pacbio | |
23 $skip_initial | |
24 reads.$ext | |
25 '${assembly}' > $polished_gfa | |
26 ]]></command> | |
27 <inputs> | |
28 <param name="reads" type="data" format="fasta,fastq,fastq.gz,fastqsanger.gz" label="Long reads for polishing"/> | |
29 <param name="assembly" type="data" format="gfa1" label="Miniasm assembly to be polished"/> | |
30 <param argument="--rounds" type="integer" min="0" value="2" label="Rounds" help="Number of full Racon polishing rounds. Default: 2" /> | |
31 <param argument="--pacbio" type="boolean" truevalue="--pacbio" falsevalue="" checked="false" label="PacBio reads" help="Use this flag for PacBio reads to make Minipolish use the map-pb | |
32 Minimap2 preset. Default: assumes Nanopore reads and uses the map-ont preset" /> | |
33 <param argument="--skip_initial" type="boolean" truevalue="--skip_initial" falsevalue="" checked="false" label="Skip the initial polishing round" help="Appropriate if the input GFA does | |
34 not have 'a' lines. Default: do the initial polishing round" /> | |
35 </inputs> | |
36 <outputs> | |
37 <data name="polished_gfa" format="gfa1" label="${tool.name} on ${on_string}: polished GFA"/> | |
38 </outputs> | |
39 <tests> | |
40 <!-- Test default parameters --> | |
41 <test expect_num_outputs="1"> | |
42 <param name="reads" value="reads.fastq"/> | |
43 <param name="assembly" value="miniasm.gfa"/> | |
44 <param name="rounds" value="2"/> | |
45 <output name="polished_gfa" file="test_01.gfa" ftype="gfa1"/> | |
46 | |
47 </test> | |
48 <!-- Test optional parameters --> | |
49 <test expect_num_outputs="1"> | |
50 <param name="reads" value="reads.fastq.gz"/> | |
51 <param name="assembly" value="miniasm.gfa"/> | |
52 <param name="rounds" value="3"/> | |
53 <param name="pacbio" value="true"/> | |
54 <param name="skip_initial" value="true"/> | |
55 <output name="polished_gfa" file="test_02.gfa" ftype="gfa1"/> | |
56 </test> | |
57 </tests> | |
58 <help><![CDATA[ | |
59 | |
60 .. class:: infomark | |
61 | |
62 **Purpose** | |
63 | |
64 Miniasm is a great long-read assembly tool: straight-forward, effective and very fast. However, it does not include a polishing step, so its assemblies have a high error rate – they are essentially made of stitched-together pieces of long reads. | |
65 | |
66 Racon is a great polishing tool that can be used to clean up assembly errors. It's also very fast and well suited for long-read data. However, it operates on FASTA files, not the GFA graphs that miniasm makes. | |
67 | |
68 That's where Minipolish comes in. With a single command, it will use Racon to polish up a miniasm assembly, while keeping the assembly in graph form. | |
69 | |
70 It also takes care of some of the other nuances of polishing a miniasm assembly: | |
71 | |
72 - Adding read depth information to contigs | |
73 - Fixing sequence truncation that can occur in Racon | |
74 - Adding circularising links to circular contigs if not already present (so they display better in Bandage) | |
75 - 'Rotating' circular contigs between polishing rounds to ensure clean circularisation | |
76 | |
77 .. class:: infomark | |
78 | |
79 **CIGARs** | |
80 | |
81 It is important to note here something that Minipolish does not do: change/fix the CIGAR strings indicating contig overlap. While circular contigs will be connected with an overlap-free link (i.e. a CIGAR of 0M), links between linear contigs will have overlap. | |
82 | |
83 So take CIGAR overlaps between polished contigs with a grain of salt. They will still indicate the approximate amount of overlap, not the exact amount. | |
84 | |
85 ]]></help> | |
86 <expand macro="citations" /> | |
87 </tool> |