diff abricate.xml @ 4:78c75f134c16 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339

--- a/abricate.xml	Mon Sep 04 02:47:12 2017 -0400
+++ b/abricate.xml	Mon Mar 19 10:42:19 2018 -0400
@@ -1,9 +1,12 @@
-<tool id="abricate" name="ABRicate" version="0.7">
-    <requirements>
-        <requirement type="package" version="0.7">abricate</requirement>
-    </requirements>
-
-    <version_command>abricate --version</version_command>
+<tool id="abricate" name="ABRicate" version="@VERSION@">
+    <description>
+        Mass screening of contigs for antimicrobial and virulence genes
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
 
     <command detect_errors="exit_code"><![CDATA[
         abricate '$file_input'
@@ -19,12 +22,13 @@
         <param name="file_input" type="data" format="fasta,genbank,embl" label="Input file (Fasta, Genbank or EMBL file)" help="To screen for antibiotic resistant genes, can be a fasta file, a genbank file or an EMBL file." />
         <section name="adv" title="Advanced options" expanded="False">
             <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
-                <option value="argannot">argannot</option>
-                <option value="card">card</option>
-                <option value="ncbibetalactamase">ncbi betalactamase</option>
-                <option value="resfinder" selected="true">resfinder</option>
-                <option value="plasmidfinder">plasmidfinder</option>
-                <option value="vfdb">vfdb</option>
+                <option value="argannot">ARG-ANNOT</option>
+                <option value="card">CARD</option>
+                <option value="ecoh">EcOH</option>
+                <option value="ncbi">NCBI Bacterial Antimicrobial Resistance Reference Gene Database</option>
+                <option value="resfinder" selected="true">Resfinder</option>
+                <option value="plasmidfinder">PlasmidFinder</option>
+                <option value="vfdb">VFDB</option>
             </param>
             <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
             <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
@@ -126,14 +130,5 @@
         6159.fna  NC_017339.1  10150   10995   blaZ_32  1-846/846    ===============  0/0   100.00     100.000    resfinder  AP004832
     ]]></help>
 
-    <citations>
-        <citation type="bibtex">
-@UNPUBLISHED{Seemann2016,
-    author = {Seemann, Torsten},
-    title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
-    year = {2016},
-    url = {https://github.com/tseemann/abricate},
-}
-        </citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>