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Update Orione citation. Add <citations> tag. Use package_muscle_3_8_31 from iuc.
author crs4
date Thu, 04 Jun 2015 11:34:04 -0400
parents ec6f5279dc01
children
comparison
equal deleted inserted replaced
0:ec6f5279dc01 1:533b3b2a1e66
1 <tool id="muscle" name="MUSCLE" version="0.0.10"> 1 <tool id="muscle" name="MUSCLE" version="0.0.11">
2 <description>multiple aligner</description> 2 <description>multiple aligner</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.8.31">muscle</requirement> 4 <requirement type="package" version="3.8.31">muscle</requirement>
5 <requirement type="set_environment">FASTA_MAX_SIZE</requirement>
5 </requirements> 6 </requirements>
6 <version_command>muscle -version</version_command> 7 <version_command>muscle -version</version_command>
7 <command> 8 <command>
8 FASTA_MAX_SIZE=\${FASTA_MAX_SIZE:-100000}; 9 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 if [ `stat -c "%s" $multifasta` -gt \$FASTA_MAX_SIZE ]; then echo "Multi-FASTA file is bigger than the configured limit for MUSCLE (\$FASTA_MAX_SIZE bytes)." >&amp;2; exit 1; fi;
22 </inputs> 23 </inputs>
23 <outputs> 24 <outputs>
24 <data name="output" format="fasta" label="${tool.name} on ${on_string}: aligned sequences"/> 25 <data name="output" format="fasta" label="${tool.name} on ${on_string}: aligned sequences"/>
25 <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/> 26 <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
26 </outputs> 27 </outputs>
28 <tests>
29 </tests>
27 <help> 30 <help>
28 **What it does** 31 **What it does**
29 32
30 This tool performs multiple sequence alignment using MUSCLE. 33 This tool performs multiple sequence alignment using MUSCLE.
31 34
32 **License and citation** 35 **License and citation**
33 36
34 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. 37 This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
35 38
36 .. _CRS4 Srl.: http://www.crs4.it/ 39 .. _CRS4 Srl.: http://www.crs4.it/
37 .. _MIT license: http://opensource.org/licenses/MIT 40 .. _MIT license: http://opensource.org/licenses/MIT
38 41
39 If you use this tool in Galaxy, please cite |Cuccuru2013|_. 42 You can use this tool only if you agree to the license terms of: `MUSCLE`_.
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 43
46 .. _MUSCLE: http://drive5.com/muscle/ 44 .. _MUSCLE: http://drive5.com/muscle/
45
46 If you use this tool, please cite:
47
48 - |Cuccuru2014|_
49 - |Edgar2004|_.
50
51 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
52 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
47 .. |Edgar2004| replace:: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. *Nucleic Acids Res.* 32(5), 1792-1797 53 .. |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 54 .. _Edgar2004: http://nar.oxfordjournals.org/content/32/5/1792
49 </help> 55 </help>
56 <citations>
57 <citation type="doi">10.1093/nar/gkh340</citation>
58 </citations>
50 </tool> 59 </tool>