comparison prokka.xml @ 7:f5e44aad6498 draft

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.

6:3ad7ef0ba385

<tool id="prokka" name="Prokka" version="1.4.0">
  <description>prokaryotic genome annotation</description>
  <requirements>
    <requirement type="package" version="2.2.28">blast+</requirement>
    <requirement type="package" version="3.1b1">hmmer</requirement>
    <requirement type="package" version="1.2.36">aragorn</requirement>
    <requirement type="package" version="2.60">prodigal</requirement>
    <requirement type="package" version="23.7">tbl2asn</requirement>
    <requirement type="package" version="20131122">gnu_parallel</requirement>
    <requirement type="package" version="0.5">barrnap</requirement>
    <requirement type="package" version="1.1">infernal</requirement>
    <requirement type="package" version="0.1.6">minced</requirement>
    <requirement type="package" version="1.10">prokka</requirement>
  </requirements>
  <version_command>prokka --version</version_command>
  <command>
    prokka
    --cpus \${GALAXY_SLOTS:-8}

.. _MIT license: http://opensource.org/licenses/MIT

You can use this tool only if you agree to the license terms of: `Prokka`_.

.. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml

If you use this tool, please cite:

- |Cuccuru2014|_
- |Seemann2014|_.

.. |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
.. |Seemann2014| replace:: Seemann, T. (2014) Prokka: rapid prokaryotic genome annotation. *Bioinformatics* 30(14), 2068-2069
.. _Seemann2014: http://bioinformatics.oxfordjournals.org/content/30/14/2068
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btu135</citation>
    <citation type="doi">10.1093/bioinformatics/btu153</citation>
  </citations>

7:f5e44aad6498

<tool id="prokka" name="Prokka" version="1.11.0">
  <description>prokaryotic genome annotation</description>
  <requirements>
    <requirement type="package" version="2.2.31">blast+</requirement>
    <requirement type="package" version="3.1b2">hmmer</requirement>
    <requirement type="package" version="1.2.36">aragorn</requirement>
    <requirement type="package" version="2.60">prodigal</requirement>
    <requirement type="package" version="24.3">tbl2asn</requirement>
    <requirement type="package" version="20131122">gnu_parallel</requirement>
    <requirement type="package" version="0.7">barrnap</requirement>
    <requirement type="package" version="1.1">infernal</requirement>
    <requirement type="package" version="0.1.6">minced</requirement>
    <requirement type="package" version="1.11">prokka</requirement>
  </requirements>
  <version_command>prokka --version</version_command>
  <command>
    prokka
    --cpus \${GALAXY_SLOTS:-8}

.. _MIT license: http://opensource.org/licenses/MIT

You can use this tool only if you agree to the license terms of: `Prokka`_.

.. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml
  </help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btu135</citation>
    <citation type="doi">10.1093/bioinformatics/btu153</citation>
  </citations>