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comparison prokka.xml @ 7:f5e44aad6498 draft

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Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3.
author crs4
date Thu, 01 Oct 2015 14:14:06 -0400
parents 3ad7ef0ba385
children 392255fa7ab9
comparison
equal deleted inserted replaced
6:3ad7ef0ba385 7:f5e44aad6498
1 <tool id="prokka" name="Prokka" version="1.4.0"> 1 <tool id="prokka" name="Prokka" version="1.11.0">
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="2.2.31">blast+</requirement>
5 <requirement type="package" version="3.1b1">hmmer</requirement> 5 <requirement type="package" version="3.1b2">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="package" version="23.7">tbl2asn</requirement> 8 <requirement type="package" version="24.3">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="0.5">barrnap</requirement> 10 <requirement type="package" version="0.7">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="0.1.6">minced</requirement> 12 <requirement type="package" version="0.1.6">minced</requirement>
13 <requirement type="package" version="1.10">prokka</requirement> 13 <requirement type="package" version="1.11">prokka</requirement>
14 </requirements> 14 </requirements>
15 <version_command>prokka --version</version_command> 15 <version_command>prokka --version</version_command>
16 <command> 16 <command>
17 prokka 17 prokka
18 --cpus \${GALAXY_SLOTS:-8} 18 --cpus \${GALAXY_SLOTS:-8}
198 .. _MIT license: http://opensource.org/licenses/MIT 198 .. _MIT license: http://opensource.org/licenses/MIT
199 199
200 You can use this tool only if you agree to the license terms of: `Prokka`_. 200 You can use this tool only if you agree to the license terms of: `Prokka`_.
201 201
202 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml 202 .. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
203
204 If you use this tool, please cite:
205
206 - |Cuccuru2014|_
207 - |Seemann2014|_.
208
209 .. |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
210 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
211 .. |Seemann2014| replace:: Seemann, T. (2014) Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 30(14), 2068-2069
212 .. _Seemann2014: http://bioinformatics.oxfordjournals.org/content/30/14/2068
213 </help> 203 </help>
214 <citations> 204 <citations>
215 <citation type="doi">10.1093/bioinformatics/btu135</citation> 205 <citation type="doi">10.1093/bioinformatics/btu135</citation>
216 <citation type="doi">10.1093/bioinformatics/btu153</citation> 206 <citation type="doi">10.1093/bioinformatics/btu153</citation>
217 </citations> 207 </citations>