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comparison kc-align.xml @ 0:ca206e09fdc7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align commit 3b23039a67d8cb2d185c56df50b837e5601a95bf"
author iuc
date Tue, 17 Mar 2020 19:23:52 +0000
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1 <tool id="kc-align" name="Kc-Align" version="0.1.0" python_template_version="3.5">
2 <requirements>
3 <requirement type="package" version="0.5">kcalign</requirement>
4 <requirement type="package" version="2.04">kalign2</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8 kc-align
9 --mode $position.mode
10 --reference '$reference'
11 --reads '$reads'
12 #if $position.mode == "genome":
13 --start $position.start
14 --end $position.end
15 #end if
16 ]]></command>
17 <inputs>
18 <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
19 <param name="reads" type="data" format="fasta" label="Reads" help="Single or multi-FASTA seqeunces to be aligned with the reference" />
20 <conditional name="position" >
21 <param name="mode" type="select" label="Mode" >
22 <option value="genome">Genome</option>
23 <option value="gene">Gene</option>
24 <option value="mixed">Mixed</option>
25 </param>
26 <when value="genome" >
27 <param name="start" type="integer" value="0" min="0" label="Start Position" help="The 1-indexed start position of the gene of interest in the reference sequence" />
28 <param name="end" type="integer" value="0" min="0" label="End Position" help="The 1-indexed end position of the gene of interest in the reference sequence" />
29 </when>
30 <when value="gene" >
31 </when>
32 <when value="mixed" >
33 </when>
34 </conditional>
35 </inputs>
36 <outputs>
37 <data name="fasta" format="fasta" from_work_dir="kc-align.fasta" label="out.fasta" />
38 <data name="clustal" format="txt" from_work_dir="kc-align.clustal" label="out.clustal" />
39 </outputs>
40 <tests>
41 <test>
42 <param name="reference" ftype="fasta" value="MN908947.3.fasta" />
43 <param name="reads" ftype="fasta" value="corona.fasta" />
44 <param name="mode" value="genome" />
45 <param name="start" value="21563" />
46 <param name="end" value="25384" />
47 <output name="fasta" ftype="fasta" compare="diff" value="kc-align.fasta" />
48 <output name="clustal" ftype="txt" compare="diff" value="kc-align.clustal" />
49 </test>
50 </tests>
51 <help><![CDATA[
52
53 ============
54 Kc-Align
55 ============
56
57 Kc-Algin is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces two outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format.
58
59 Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout.
60
61 Modes:
62 ------
63
64 Kc-Align can be run in three different modes, depending on your input data.
65
66 * In **genome** mode, the "reference" and "reads" input parameters are all full genome FASTA files. This mode also requires the 1-based start and end position numbers corresponding to the gene you are interested in aligning from the reference input.
67
68 * If both the "reference" and "reads" inputs are already in-frame genes, the **gene** mode should be used. This mode does not require start and end position parameters as the reference is already in-frame.
69
70 * For the case when your "reference" is an in-frame gene while the "reads" are whole genomes, the **mixed** mode can be used. Like gene mode, this mode does not require the start and end point position parameters.
71
72
73 ]]></help>
74 <citations>
75 <citation type="bibtex">
76 @misc{githubkcalign,
77 author = {Nicholas Keener, Emil Bouvier},
78 year = {2020},
79 title = {Kc-Align},
80 publisher = {Github},
81 journal = {Github repository},
82 url = {https://github.com/davebx/kc-align},
83 }</citation>
84 </citations>
85 </tool>