Mercurial > repos > crs4 > muscle
diff muscle.xml @ 1:533b3b2a1e66 draft default tip
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 |
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--- a/muscle.xml Wed Oct 30 07:34:04 2013 -0400 +++ b/muscle.xml Thu Jun 04 11:34:04 2015 -0400 @@ -1,7 +1,8 @@ -<tool id="muscle" name="MUSCLE" version="0.0.10"> +<tool id="muscle" name="MUSCLE" version="0.0.11"> <description>multiple aligner</description> <requirements> <requirement type="package" version="3.8.31">muscle</requirement> + <requirement type="set_environment">FASTA_MAX_SIZE</requirement> </requirements> <version_command>muscle -version</version_command> <command> @@ -24,6 +25,8 @@ <data name="output" format="fasta" label="${tool.name} on ${on_string}: aligned sequences"/> <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/> </outputs> + <tests> + </tests> <help> **What it does** @@ -31,20 +34,26 @@ **License and citation** -This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. +This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ .. _MIT license: http://opensource.org/licenses/MIT -If you use this tool in Galaxy, please cite |Cuccuru2013|_. - -.. |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* -.. _Cuccuru2013: http://orione.crs4.it/ - -This tool uses `MUSCLE`_, which is licensed separately. Please cite |Edgar2004|_. +You can use this tool only if you agree to the license terms of: `MUSCLE`_. .. _MUSCLE: http://drive5.com/muscle/ + +If you use this tool, please cite: + +- |Cuccuru2014|_ +- |Edgar2004|_. + +.. |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 +.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928 .. |Edgar2004| replace:: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. *Nucleic Acids Res.* 32(5), 1792-1797 .. _Edgar2004: http://nar.oxfordjournals.org/content/32/5/1792 </help> + <citations> + <citation type="doi">10.1093/nar/gkh340</citation> + </citations> </tool>