diff abricate_list.xml @ 0:862f5a86854d draft

planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abricate_list.xml	Tue Nov 29 14:52:34 2016 -0500
@@ -0,0 +1,44 @@
+<tool id="abricate_list" name="ABRicate List" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="0.3">abricate</requirement>
+        <requirement type="package" version="5.18.1">perl</requirement>
+        <requirement type="package" version="2.2.31">blast+</requirement>
+    </requirements>
+
+    <version_command>abricate --version</version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+        abricate --list 2> "$report"
+    ]]></command>
+
+    <inputs>
+
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="report" label="${tool.name} - list of databases"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <output name="report" ftype="txt" file="output_list.txt" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+ABRicate List will list all the antibiotic databases used by ABRicate. The database of these genes is built from ResFinder.
+
+    ]]></help>
+
+    <citations>
+      <citation type="bibtex">
+        @UNPUBLISHED{Seemann2016,
+        author = "Seemann T",
+        title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
+        year = "2016",
+        note = "https://github.com/tseemann/abricate"}
+      </citation>
+    </citations>
+</tool>