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changeset 5:930893c83a1a draft

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planemo upload for repository https://github.com/phac-nml/staramr commit 0794053d021c92d4dd7459abca46d4bf823d7203
author nml
date Tue, 19 Feb 2019 16:47:25 -0500
parents 1e8ec0f861ff
children 3c09557ac425
files staramr_search.xml
diffstat 1 files changed, 8 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- 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