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comparison muscle.xml @ 0:ec6f5279dc01 draft

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author crs4
date Wed, 30 Oct 2013 07:34:04 -0400
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-1:000000000000 0:ec6f5279dc01
1 <tool id="muscle" name="MUSCLE" version="0.0.10">
2 <description>multiple aligner</description>
3 <requirements>
4 <requirement type="package" version="3.8.31">muscle</requirement>
5 </requirements>
6 <version_command>muscle -version</version_command>
7 <command>
8 FASTA_MAX_SIZE=\${FASTA_MAX_SIZE:-100000};
9 if [ `stat -c "%s" $multifasta` -gt \$FASTA_MAX_SIZE ]; then echo "Multi-FASTA file is bigger than the configured limit for MUSCLE (\$FASTA_MAX_SIZE bytes)." >&amp;2; exit 1; fi;
10 muscle -quiet -in $multifasta -out $output -log $log
11 #if str($maxiters)
12 -maxiters $maxiters
13 #end if
14 #if $diags
15 -diags
16 #end if
17 </command>
18 <inputs>
19 <param name="multifasta" type="data" format="fasta" label="Multi-FASTA file" />
20 <param name="maxiters" type="integer" value="2" min="1" max="16" optional="true" label="Maximum number of iterations to run (-maxiters)" help="Set to 2 for large datasets where refinement (iterations 3+) is too slow." />
21 <param name="diags" type="boolean" label="Diagonal optimization (-diags)" help="Speed up the algorithm, especially for closely related sequences, at the expense of some reduction in accuracy" />
22 </inputs>
23 <outputs>
24 <data name="output" format="fasta" label="${tool.name} on ${on_string}: aligned sequences"/>
25 <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
26 </outputs>
27 <help>
28 **What it does**
29
30 This tool performs multiple sequence alignment using MUSCLE.
31
32 **License and citation**
33
34 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
35
36 .. _CRS4 Srl.: http://www.crs4.it/
37 .. _MIT license: http://opensource.org/licenses/MIT
38
39 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
40
41 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
42 .. _Cuccuru2013: http://orione.crs4.it/
43
44 This tool uses `MUSCLE`_, which is licensed separately. Please cite |Edgar2004|_.
45
46 .. _MUSCLE: http://drive5.com/muscle/
47 .. |Edgar2004| replace:: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. *Nucleic Acids Res.* 32(5), 1792-1797
48 .. _Edgar2004: http://nar.oxfordjournals.org/content/32/5/1792
49 </help>
50 </tool>