# HG changeset patch
# User nml
# Date 1550612845 18000
# Node ID 930893c83a1acc0de5f571654f47d7e18f9ea5af
# Parent  1e8ec0f861ff2631ae045614bf7a298f0c6e3a7b
planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203

diff -r 1e8ec0f861ff -r 930893c83a1a staramr_search.xml
--- a/staramr_search.xml	Thu Nov 22 13:38:58 2018 -0500
+++ b/staramr_search.xml	Tue Feb 19 16:47:25 2019 -0500
@@ -1,8 +1,12 @@
-<tool id="staramr_search" name="staramr" version="0.3.0">
+<tool id="staramr_search" name="staramr" version="@VERSION@">
     <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description>
+    <macros>
+	    <token name="@VERSION@">0.4.0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="0.3.0">staramr</requirement>
+        <requirement type="package" version="@VERSION@">staramr</requirement>
     </requirements>
+    <version_command>staramr --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
         #import re
 
@@ -57,6 +61,7 @@
             <when value="true">
                 <param name="organism" type="select" label="Select a pointfinder organism">
                     <option value="salmonella" selected="true">Salmonella</option>
+                    <option value="campylobacter">Campylobacter</option>
                 </param>
             </when>
             <when value="false" />
@@ -164,7 +169,7 @@
 -----
 
 1. Select your genome contigs (in FASTA format).
-2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* is supported).
+2. Select whether or not you wish to scan your genome for point mutations giving antimicrobial resistance using the PointFinder database. This requires you to specify the specific organism you are scanning (currently only *salmonella* and *campylobacter* is supported).
 3. Run the tool.
 
 Input