| Previous changeset 17:111884f0d912 (2020-06-04) Next changeset 19:8a22554cdde2 (2021-11-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486" |
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modified:
prokka.xml |
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| diff -r 111884f0d912 -r d643e3b03500 prokka.xml --- a/prokka.xml Thu Jun 04 07:05:17 2020 -0400 +++ b/prokka.xml Sat Feb 13 11:58:58 2021 +0000 |
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| @@ -1,7 +1,11 @@ -<tool id="prokka" name="Prokka" version="1.14.5+galaxy0"> +<tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>Prokaryotic genome annotation</description> + <macros> + <token name="@TOOL_VERSION@">1.14.6</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> <requirements> - <requirement type="package" version="1.14.5">prokka</requirement> + <requirement type="package" version="@TOOL_VERSION@">prokka</requirement> </requirements> <version_command>prokka --version</version_command> @@ -74,15 +78,16 @@ ]]></command> <inputs> <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> - <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)"> + <param argument="--locustag" type="text" value="" label="Locus tag prefix" /> + <param argument="--increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment" /> + <param argument="--gffver" type="select" label="GFF version"> <option value="3">3</option> <option value="2">2</option> <option value="1">1</option> </param> <conditional name="compliant"> - <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance (--compliant)" help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below)"> + <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance" + help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below) (--compliant)"> <option value="no">No</option> <option value="yes">Yes</option> </param> @@ -92,22 +97,22 @@ </when> <when value="yes" /> </conditional> - <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)" /> + <param argument="--centre" type="text" value="" label="Sequencing centre ID" /> + <param argument="--genus" type="text" value="" label="Genus name" help="May be used to aid annotation, see --usegenus below" /> + <param argument="--species" type="text" value="" label="Species name" /> + <param argument="--strain" type="text" value="" label="Strain name" /> + <param argument="--plasmid" type="text" value="" label="Plasmid name or identifier" /> <conditional name="kingdom"> - <param name="kingdom_select" type="select" label="Kingdom (--kingdom)"> + <param name="kingdom_select" type="select" label="Kingdom" help="(--kingdom)"> <option value="Archaea">Archaea</option> <option value="Bacteria" selected="true">Bacteria</option> <option value="Viruses">Viruses</option> </param> <when value="Archaea"> - <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> + <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> </when> <when value="Bacteria"> - <param name="gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> + <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)"> <option selected="true" value="none">N/A</option> <option value="pos">positive</option> @@ -115,17 +120,17 @@ </param> SignalP is not FOSS --> </when> <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 --> + <param argument="--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" min="0" optional="true" label="Similarity e-value cut-off" /> - <param name="rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (--rfam)" /> - <param name="norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" /> - <param name="notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" /> + <param argument="--usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database" help="Will use the BLAST database for the genus specified above, if installed" /> + <param argument="--proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from" /> + <param argument="--metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes" help="Will set --meta option for Prodigal" /> + <param argument="--fast" type="boolean" checked="false" label="Fast mode" help="Skip CDS /product searching" /> + <param argument="--evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" /> + <param argument="--rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" /> + <param argument="--norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" /> + <param argument="--notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" /> <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs"> <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option> |