Mercurial > repos > crs4 > prokka
diff prokka.xml @ 14:eaee459f3d69 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9019ffd38b2b6692fc24c9b41ab2c2539050b01f
author | iuc |
---|---|
date | Wed, 28 Mar 2018 12:38:42 -0400 |
parents | a17498c603ec |
children | 3a0bd09a41dd |
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--- a/prokka.xml Tue Mar 21 10:13:06 2017 -0400 +++ b/prokka.xml Wed Mar 28 12:38:42 2018 -0400 @@ -1,14 +1,11 @@ -<tool id="prokka" name="Prokka" version="1.12.0"> - <description>prokaryotic genome annotation</description> +<tool id="prokka" name="Prokka" version="1.13"> + <description>Prokaryotic genome annotation</description> <requirements> - <requirement type="package" version="1.12">prokka</requirement> + <requirement type="package" version="1.13">prokka</requirement> </requirements> - <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) --> - <stdio> - <exit_code range="1:" /> - </stdio> + <version_command>prokka --version</version_command> - <command><![CDATA[ + <command detect_errors="exit_code"><![CDATA[ prokka --cpus \${GALAXY_SLOTS:-8} --quiet ## to avoid non-error messages written to stderr @@ -77,7 +74,7 @@ ]]></command> <inputs> <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> - <param name="locustag" type="text" value="PROKKA" label="Locus tag prefix (--locustag)" /> + <param name="locustag" type="text" value="" label="Locus tag prefix (--locustag)" /> <param name="increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment (--increment)" /> <param name="gffver" type="select" label="GFF version (--gffver)"> <option value="3">3</option> @@ -139,6 +136,7 @@ <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc. (.sqn)</option> <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option> <option value="tbl" selected="True">Feature Table file (.tbl)</option> + <option value="tsv" selected="True">Annotations in tabular format including COGs etc.</option> <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option> <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option> </param> @@ -169,6 +167,9 @@ <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl"> <filter>outputs and 'tbl' in outputs</filter> </data> + <data name="out_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv" from_work_dir="outdir/prokka.tsv"> + <filter>outputs and 'tsv' in outputs</filter> + </data> <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err"> <filter>outputs and 'err' in outputs</filter> </data> @@ -180,7 +181,7 @@ <tests> <test> <param name="input" ftype="fasta" value="phiX174.fasta" /> - <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,err,txt" /> + <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" /> <output name="out_gff" file="out.gff" /> <output name="out_gbk" file="out.gbk" lines_diff="14" /> <output name="out_fna" file="out.fna" /> @@ -189,6 +190,7 @@ <output name="out_sqn" file="out.sqn" lines_diff="84" /> <output name="out_fsa" file="out.fsa" /> <output name="out_tbl" file="out.tbl" /> + <output name="out_tsv" file="out.tsv" /> <output name="out_err" file="out.err" /> <output name="out_txt" file="out.txt" /> <output name="out_log"> @@ -211,7 +213,7 @@ **License and citation** -This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_ and is released under the `MIT license`_. +This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_, 2018 `Galaxy IUC` and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ .. _Earlham Institute: http://earlham.ac.uk/