prokka: prokka.xml comparison

comparison prokka.xml @ 6:3ad7ef0ba385 draft

Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.

author	crs4
date	Mon, 27 Oct 2014 06:45:52 -0400
parents	5c0030f52b83
children	f5e44aad6498

comparison

equal deleted inserted replaced

-:b9fea998270a
+:3ad7ef0ba385
-<tool id="prokka" name="Prokka" version="1.3.0">
+<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="22.4">tbl2asn</requirement>
+<requirement type="package" version="23.7">tbl2asn</requirement>
 <requirement type="package" version="20131122">gnu_parallel</requirement>
-<requirement type="package" version="0.3">barrnap</requirement>
+<requirement type="package" version="0.5">barrnap</requirement>
 <requirement type="package" version="1.1">infernal</requirement>
-<requirement type="package" version="0.1.4">minced</requirement>
+<requirement type="package" version="0.1.6">minced</requirement>
-<requirement type="package" version="1.8">prokka</requirement>
+<requirement type="package" version="1.10">prokka</requirement>
 </requirements>
 <version_command>prokka --version</version_command>
 <command>
 prokka
 --cpus \${GALAXY_SLOTS:-8}
 --gcode $kingdom.gcode
 #end if
 #if $usegenus
 --usegenus
 #end if
+#if $proteins
+--proteins $proteins
+#end if
 #if $metagenome
 --metagenome
 #end if
 #if $fast
 --fast
 #if $notrna
 --notrna
 #end if
 $input
 </command>
+<!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) -->
+<stdio>
+<exit_code range="1:" />
+</stdio>
 <inputs>
 <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" />
-<param name="locustag" type="text" value="PROKKA" optional="true" label="Locus tag prefix (--locustag)" />
+<param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" />
 <param name="increment" type="integer" value="1" optional="true" label="Locus tag counter increment (--increment)">
 <validator type="in_range" min="1" />
 </param>
 <param name="gffver" type="select" label="GFF version (--gffver)">
 <option value="3">3</option>
 <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" />
 <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" />
 </when>
 <when value="yes" />
 </conditional>
-<param name="centre" type="text" value="" optional="true" label="Sequencing centre ID (--centre)" />
+<param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" />
-<param name="genus" type="text" value="" optional="true" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
+<param name="genus" type="text" value="" label="Genus name (--genus)" help="May be used to aid annotation, see --usegenus below" />
-<param name="species" type="text" value="" optional="true" label="Species name (--species)" />
+<param name="species" type="text" value="" label="Species name (--species)" />
-<param name="strain" type="text" value="" optional="true" label="Strain name (--strain)" />
+<param name="strain" type="text" value="" label="Strain name (--strain)" />
-<param name="plasmid" type="text" value="" optional="true" label="Plasmid name or identifier (--plasmid)" />
+<param name="plasmid" type="text" value="" label="Plasmid name or identifier (--plasmid)" />
 <conditional name="kingdom">
 <param name="kingdom_select" type="select" label="Kingdom (--kingdom)">
 <option value="Archaea">Archaea</option>
 <option value="Bacteria" selected="true">Bacteria</option>
 <option value="Viruses">Viruses</option>
 <when value="Viruses">
 <param name="gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash -->
 </when>
 </conditional>
 <param name="usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database (--usegenus)" help="Will use the BLAST database for the genus specified above, if installed" />
+<param name="proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from (--proteins)" />
 <param name="metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes (--metagenome)" help="Will set --meta option for Prodigal" />
 <param name="fast" type="boolean" checked="false" label="Fast mode (--fast)" help="Skip CDS /product searching" />
 <param name="evalue" type="float" value="1e-06" optional="true" label="Similarity e-value cut-off">
 <validator type="in_range" min="0" />
 </param>
 txt
 Statistics relating to the annotated features found
 **License and citation**
-This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_, Lionel Guy and is released under the `MIT license`_.
+This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_, © 2013 Lionel Guy 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|_.
+You can use this tool only if you agree to the license terms of: `Prokka`_.
-.. |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 `Prokka`_, which is licensed separately. Please cite Seemann, T. (2013) Prokka: Rapid Prokaryotic Genome Annotation. *Submitted*
 .. _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>
 </tool>

Mercurial > repos > crs4 > prokka

comparison prokka.xml @ 6:3ad7ef0ba385 draft