Mercurial > repos > iuc > berokka

annotate berokka.xml @ 2:20d30fa68f08 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0bd65eaa95eb597eae30b6feef63000901ed8230"
author iuc
date Thu, 25 Nov 2021 14:22:03 +0000
parents 7a2f5743b1cf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
7a2f5743b1cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0f23197bb8b21c1499d8afa6d22c071dfa296a0f"
iuc
parents: 0
diff changeset
1 <tool id="berokka" name="Berokka" version="@TOOL_VERSION@" profile="19.01">
0
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
2 <description>Trim, circularise, orient and filter long read bacterial genome assemblies</description>
1
7a2f5743b1cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0f23197bb8b21c1499d8afa6d22c071dfa296a0f"
iuc
parents: 0
diff changeset
3 <macros>
7a2f5743b1cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0f23197bb8b21c1499d8afa6d22c071dfa296a0f"
iuc
parents: 0
diff changeset
4 <token name="@TOOL_VERSION@">0.2.3</token>
7a2f5743b1cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0f23197bb8b21c1499d8afa6d22c071dfa296a0f"
iuc
parents: 0
diff changeset
5 </macros>
0
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
6 <requirements>
1
7a2f5743b1cf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 0f23197bb8b21c1499d8afa6d22c071dfa296a0f"
iuc
parents: 0
diff changeset
7 <requirement type="package" version="@TOOL_VERSION@">berokka</requirement>
0
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
8 </requirements>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
10 berokka
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
11 --outdir default '${input_file}'
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
12
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
13 #if $filter_fasta:
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
14 --filter '${filter_fasta}'
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
15 #end if
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
16
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
17 --readlen '${read_length}'
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
18
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
19 --fuzz '${fuzz}'
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
20
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
21 #unless $anno:
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
22 --noanno
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
23 #end unless
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
24
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
25 ]]></command>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
26 <inputs>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
27 <param name="input_file" type="data" format="fasta" label="Input (FASTA)" help="Should be completed long-read assemblies in FASTA format, such as those from CANU or HGAP"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
28 <param name="filter_fasta" optional="true" type="data" format="fasta" label="Filter (FASTA)" help="Give a fasta to use as a filter."/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
29 <param name="read_length" type="integer" value="60000" min="28" label="Read Length" help="Approximate max read length (default '60000')"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
30 <param name="fuzz" type="integer" value="5" label="Fuzz" help="Accept local alignment within X bp of global (default '5')"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
31 <param name="anno" type="boolean" checked="true" label="Annotation" help="Annotate Trimmed FASTA"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
32 </inputs>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
33 <outputs>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
34 <data name="trimmed" format="fasta" from_work_dir="default/02.trimmed.fa" label="${tool.name} on ${on_string}: Trimmed"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
35 <data name="results" format="tabular" from_work_dir="default/03.results.tab" label="${tool.name} on ${on_string}: Results"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
36 </outputs>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
37 <tests>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
38 <test>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
39 <param name="input_file" value="berokka_test1.fasta"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
40 <param name="read_length" value="60000"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
41 <param name="fuzz" value="5"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
42 <param name="anno" value="true"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
43 <output name="trimmed" file="trimmed_1" ftype="fasta"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
44 <output name="results" file="results_1" ftype="tabular"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
45 </test>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
46 <test>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
47 <param name="input_file" value="berokka_test1.fasta"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
48 <param name="filter_fasta" value="berokka_test1.fasta"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
49 <param name="read_length" value="60000"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
50 <param name="fuzz" value="5"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
51 <param name="anno" value="true"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
52 <output name="trimmed" file="trimmed_2" ftype="fasta"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
53 <output name="results" file="results_2" ftype="tabular"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
54 </test>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
55 <test>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
56 <param name="input_file" value="berokka_test1.fasta"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
57 <param name="read_length" value="100"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
58 <param name="fuzz" value="50"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
59 <param name="anno" value="false"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
60 <output name="trimmed" file="trimmed_3" ftype="fasta"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
61 <output name="results" file="results_3" ftype="tabular"/>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
62 </test>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
63 </tests>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
64 <help><![CDATA[
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
65 **Summary**
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
66
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
67 Trim, circularise, orient & filter long read bacterial genome assemblies
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
68 There is already a good piece of software to trim/circularise and orient genome assemblies called Circlator. Please try that first!
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
69
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
70 You should only try Berokka if:
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
71
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
72 1. You only have the contig files and do not have the corrected reads anymore
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
73 2. Your contigs are simple cases with clear overhang and could be done manually with BLAST
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
74 3. Circlator fails on your data even after troubleshooting
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
75
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
76 NOTE: orientation to dnaA or rep genes is not yet implemented.
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
77
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
78 **Input**
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
79
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
80 Input should be completed long-read assemblies in FASTA format, such as those from CANU or HGAP.
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
81
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
82 **Output**
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
83
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
84 1. trimmed: The (possibly) trimmed sequences (FASTA)
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
85
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
86 2. results: Summary of results (TSV)
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
87
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
88 **Options**
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
89
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
90 * `Filter <FASTA>` allows you to remove contigs which match 50% of sequences in this file. Berokka comes with the standard Pacbio control sequence. You can provide your own FASTA file using this option.
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
91
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
92 * `Read Length <LENGTH>` can be used for datasets that won't seem to circularise. It affects the length of the match it attempts to make using BLAST.
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
93
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
94 * `Fuzz` can be used to accept local alignment within X bp of global (default '5')
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
95
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
96 * `Annotation` can be set to "No" to ensure that the FASTA descriptions are not altered between the input and output FASTA files.
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
97
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
98 ]]></help>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
99 <citations>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
100 <citation type="bibtex">
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
101 @UNPUBLISHED{Seemann2016,
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
102 author = {Seemann, Torsten},
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
103 title = {Berokka: Faster Trim, circularise and orient long read bacterial genome assemblies},
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
104 year = {2016},
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
105 url = {https://github.com/tseemann/berokka},
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
106 }
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
107 </citation>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
108 </citations>
41a67d35f977 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/berokka commit 387f04ffbf5205aaaa7b46e9e3d518edb62a538f
iuc
parents:
diff changeset
109 </tool>