Mercurial > repos > crs4 > prokka
changeset 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 | b9fea998270a |
children | f5e44aad6498 |
files | COPYING prokka.xml readme.rst tool_dependencies.xml |
diffstat | 4 files changed, 57 insertions(+), 38 deletions(-) [+] |
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--- a/COPYING Thu Jan 09 16:49:50 2014 -0500 +++ b/COPYING Mon Oct 27 06:45:52 2014 -0400 @@ -4,6 +4,7 @@ Paolo Uva <paolo.uva@crs4.it> Nicola Soranzo <nicola.soranzo@crs4.it> Lionel Guy <lionel.guy@icm.uu.se> +Philip Mabon <philipmabon@gmail.com> Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the
--- a/prokka.xml Thu Jan 09 16:49:50 2014 -0500 +++ b/prokka.xml Mon Oct 27 06:45:52 2014 -0400 @@ -1,16 +1,16 @@ -<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="1.8">prokka</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> @@ -57,6 +57,9 @@ #if $usegenus --usegenus #end if + #if $proteins + --proteins $proteins + #end if #if $metagenome --metagenome #end if @@ -77,9 +80,13 @@ #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> @@ -99,11 +106,11 @@ </when> <when value="yes" /> </conditional> - <param name="centre" type="text" value="" optional="true" 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="species" type="text" value="" optional="true" label="Species name (--species)" /> - <param name="strain" type="text" value="" optional="true" label="Strain name (--strain)" /> - <param name="plasmid" type="text" value="" optional="true" label="Plasmid name or identifier (--plasmid)" /> + <param name="centre" type="text" value="" label="Sequencing centre ID (--centre)" /> + <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="" label="Species name (--species)" /> + <param name="strain" type="text" value="" label="Strain name (--strain)" /> + <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> @@ -126,6 +133,7 @@ </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"> @@ -184,18 +192,27 @@ **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|_. - -.. |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* +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> </tool>
--- a/readme.rst Thu Jan 09 16:49:50 2014 -0500 +++ b/readme.rst Mon Oct 27 06:45:52 2014 -0400 @@ -4,9 +4,9 @@ Warning ------- -Prokka includes custom databases and is thus about a 2.0 GB download! +Prokka includes custom databases and is thus about a 340 MB download! -Dependencies of Prokka which needs to be installed separately +Dependencies of Prokka which need to be installed separately ------------------------------------------------------------- - Perl core modules: File\::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds; @@ -20,7 +20,7 @@ Configuration ------------- -prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see http://wiki.galaxyproject.org/Admin/Config/Jobs and http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). +prokka tool may be configured to use more than one CPU core by selecting an appropriate destination for this tool in Galaxy job_conf.xml file (see https://wiki.galaxyproject.org/Admin/Config/Jobs and https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ). If you are using Galaxy release_2013.11.04 or later, this tool will automatically use the number of CPU cores allocated by the job runner according to the configuration of the destination selected for this tool. @@ -30,11 +30,12 @@ (where N is the number of CPU cores allocated by the job runner for this tool) to the file - <tool_dependencies_dir>/prokka/1.7/crs4/prokka/<hash_string>/env.sh + <tool_dependencies_dir>/prokka/1.10/crs4/prokka/<hash_string>/env.sh Version history --------------- +- Release 6 (prokka 1.4.0): 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>. - Release 5 (prokka 1.3.0): Fix Prokka 1.8 dependency installation. - Release 4 (prokka 1.3.0): Support Prokka 1.8. Depend on package_minced_0_1_4 and package_tbl2asn_22_4 (requires Galaxy release_2013.11.04 or later). Update citation. - Release 3 (prokka 1.2.0): Use $GALAXY_SLOTS instead of $PROKKA_SITE_OPTIONS. Upgrade Barrnap dependency to v. 0.3. Upgrade Infernal dependency to v. 1.1. Depend on package_gnu_parallel_20131122 (requires Galaxy release_2013.11.04 or later).
--- a/tool_dependencies.xml Thu Jan 09 16:49:50 2014 -0500 +++ b/tool_dependencies.xml Mon Oct 27 06:45:52 2014 -0400 @@ -1,37 +1,37 @@ <?xml version="1.0"?> <tool_dependency> <package name="blast+" version="2.2.28"> - <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="hmmer" version="3.1b1"> - <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="aragorn" version="1.2.36"> - <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="prodigal" version="2.60"> - <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="tbl2asn" version="22.4"> - <repository changeset_revision="55f52e5395cd" name="package_tbl2asn_22_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="tbl2asn" version="23.7"> + <repository changeset_revision="2271d52a8531" name="package_tbl2asn_23_7" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="gnu_parallel" version="20131122"> - <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="barrnap" version="0.3"> - <repository changeset_revision="60763b9e2026" name="package_barrnap_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="barrnap" version="0.5"> + <repository changeset_revision="ec528d56b01f" name="package_barrnap_0_5" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="infernal" version="1.1"> - <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="minced" version="0.1.4"> - <repository changeset_revision="0cf9719bfe4b" name="package_minced_0_1_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="minced" version="0.1.6"> + <repository changeset_revision="a135862cd007" name="package_minced_0_1_6" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="prokka" version="1.8"> + <package name="prokka" version="1.10"> <install version="1.0"> <actions> - <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action> - <action target_filename="bin/prokka" type="download_file">http://www.vicbioinformatics.com/prokka-1.8</action> + <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action> + <action type="shell_command">bin/prokka --setupdb</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> @@ -42,7 +42,7 @@ </actions> </install> <readme> -Warning: Prokka includes custom databases and is thus about a 2.0 GB download! +Warning: Prokka includes custom databases and is thus about a 340 MB download! Dependencies of Prokka which needs to be installed separately: - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;