|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool id="pipelign" name="Automated multiple sequence" version="@VERSION@+galaxy0">
|
|
|
3 <description>alignment with pipelign</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@VERSION@">0.2</token>
|
|
|
6 </macros>
|
|
|
7 <requirements>
|
|
|
8 <requirement type="package" version="@VERSION@">pipelign</requirement>
|
|
|
9 </requirements>
|
|
|
10 <command detect_errors="exit_code"><![CDATA[
|
|
|
11 pipelign -d files -c -i '$inFile' -o '$outFile' -t $lenThr -a $alphabet
|
|
|
12 -p $simPer -r $run -e $merge -q \${GALAXY_SLOTS:-1}
|
|
|
13 -s $mIterateLong -m $mIterateMerge -w $ambigPer
|
|
|
14 $keepOrphans $keepBadSeqs $excludeClusters
|
|
|
15 ]]></command>
|
|
|
16 <inputs>
|
|
|
17 <param argument="--inFile" type="data" format="fasta" label="Input sequence file" />
|
|
|
18 <param argument="--lenThr" type="float" value="0.7" min="0" max="1" label="Length threshold for full sequences" help="Default: 0.7" />
|
|
|
19 <param argument="--alphabet" type="select" label="Alphabet for input sequences">
|
|
|
20 <option value="dna">DNA</option>
|
|
|
21 <option value="rna">RNA</option>
|
|
|
22 <option value="aa">Amino Acids</option>
|
|
|
23 </param>
|
|
|
24 <param argument="--keepOrphans" type="boolean" truevalue="--keepOrphans" falsevalue="" label="Add fragments without clusters" />
|
|
|
25 <param argument="--keepBadSeqs" type="boolean" truevalue="--keepBadSeqs" falsevalue="" label="Add long sequences with too many ambiguous residues" />
|
|
|
26 <param argument="--simPer" type="float" value="0.8" min="0" max="1" label="Percent sequence similarity for clustering" help="Default: 0.8" />
|
|
|
27 <param argument="--run" type="select" label="Parallelization version">
|
|
|
28 <option value="J">Joblib</option>
|
|
|
29 <option value="G">GNU</option>
|
|
|
30 </param>
|
|
|
31 <param argument="--merge" type="select" label="Merge strategy">
|
|
|
32 <option value="P">Parallel</option>
|
|
|
33 <option value="C">Consensus</option>
|
|
|
34 </param>
|
|
|
35 <param argument="--mIterateLong" type="integer" value="1" label="Number of iterations to refine long alignments" help="Default: 1" />
|
|
|
36 <param argument="--mIterateMerge" type="integer" value="1" label="Number of iterations to refine merged alignment" help="Default: 1" />
|
|
|
37 <param argument="--ambigPer" type="float" value="0.1" min="0" max="1" label="Percent sequence similarity for clustering" help="Default: 0.1" />
|
|
|
38 <param argument="--excludeClusters" type="boolean" truevalue="--excludeClusters" falsevalue="" label="Exclude clusters from final alignment" />
|
|
|
39 </inputs>
|
|
|
40 <outputs>
|
|
|
41 <data name="outFile" format="fasta" />
|
|
|
42 </outputs>
|
|
|
43 <tests>
|
|
|
44 <test>
|
|
|
45 <param name="inFile" value="pipelign-in1.fasta" />
|
|
|
46 <output name="outFile" file="pipelign-out1.fasta" compare="sim_size" />
|
|
|
47 </test>
|
|
|
48 </tests>
|
|
|
49 <help><![CDATA[
|
|
|
50 .. class:: infomark
|
|
|
51
|
|
|
52 **What it does**
|
|
|
53
|
|
|
54 -------------------
|
|
|
55
|
|
|
56 A pipeline for automated multiple sequence alignment, particularly of viral sequences.
|
|
|
57
|
|
|
58 ]]>
|
|
|
59 </help>
|
|
|
60 <citations>
|
|
|
61 <citation type="bibtex">
|
|
|
62 @UNPUBLISHED{spond,
|
|
|
63 author = "A.S.Md.M. Hossain, S.D.W.Frost",
|
|
|
64 title = "Pipelign: an alignment pipeline for viral sequences.",
|
|
|
65 year = "2019",
|
|
|
66 note = "https://github.com/asmmhossain/pipelign/",
|
|
|
67 url = "https://github.com/asmmhossain/pipelign/"}
|
|
|
68 </citation>
|
|
|
69 </citations>
|
|
|
70 </tool>
|
