# HG changeset patch
# User iuc
# Date 1613217538 0
# Node ID d643e3b035001ac5af953154c2f9c50a4d498b2c
# Parent  111884f0d91259619646a18e1c3e9d3bb351d5ca
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 442b1247ee31ec9872633be18784f346e4762486"

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
@@ -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>