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comparison prokka.xml @ 4:5c0030f52b83 draft

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Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 . Update citation.
author crs4
date Wed, 08 Jan 2014 04:29:37 -0500
parents fffa1ae330ae
children 3ad7ef0ba385
comparison
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3:fffa1ae330ae 4:5c0030f52b83
1 <tool id="prokka" name="Prokka" version="1.2.0"> 1 <tool id="prokka" name="Prokka" version="1.3.0">
2 <description>prokaryotic genome annotation</description> 2 <description>prokaryotic genome annotation</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.2.28">blast+</requirement> 4 <requirement type="package" version="2.2.28">blast+</requirement>
5 <requirement type="package" version="3.1b1">hmmer</requirement> 5 <requirement type="package" version="3.1b1">hmmer</requirement>
6 <requirement type="package" version="1.2.36">aragorn</requirement> 6 <requirement type="package" version="1.2.36">aragorn</requirement>
7 <requirement type="package" version="2.60">prodigal</requirement> 7 <requirement type="package" version="2.60">prodigal</requirement>
8 <requirement type="binary">tbl2asn</requirement> 8 <requirement type="package" version="22.4">tbl2asn</requirement>
9 <requirement type="package" version="20131122">gnu_parallel</requirement> 9 <requirement type="package" version="20131122">gnu_parallel</requirement>
10 <requirement type="package" version="0.3">barrnap</requirement> 10 <requirement type="package" version="0.3">barrnap</requirement>
11 <requirement type="package" version="1.1">infernal</requirement> 11 <requirement type="package" version="1.1">infernal</requirement>
12 <requirement type="package" version="1.7">prokka</requirement> 12 <requirement type="package" version="0.1.4">minced</requirement>
13 <requirement type="package" version="1.8">prokka</requirement>
13 </requirements> 14 </requirements>
14 <version_command>prokka --version</version_command> 15 <version_command>prokka --version</version_command>
15 <command> 16 <command>
16 prokka 17 prokka
17 --cpus \${GALAXY_SLOTS:-8} 18 --cpus \${GALAXY_SLOTS:-8}
191 If you use this tool in Galaxy, please cite |Cuccuru2013|_. 192 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
192 193
193 .. |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* 194 .. |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*
194 .. _Cuccuru2013: http://orione.crs4.it/ 195 .. _Cuccuru2013: http://orione.crs4.it/
195 196
196 This tool uses `Prokka`_, which is licensed separately. Please cite Seemann T. Prokka: Prokaryotic Genome Annotation System (in preparation). 197 This tool uses `Prokka`_, which is licensed separately. Please cite Seemann, T. (2013) Prokka: Rapid Prokaryotic Genome Annotation. *Submitted*
197 198
198 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml 199 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
199 </help> 200 </help>
200 </tool> 201 </tool>