--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clamlst_import.xml	Thu Jun 16 12:32:28 2022 +0000
@@ -0,0 +1,56 @@
+<tool id="clamlst_import_wrapper" name="Import MLST database" version="2.1.3">
+  <description></description>
+  <requirements>
+	<requirement type="package" version="2.1.3">pymlst</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+  <version_command>claMLST -v</version_command>
+  <command>
+    claMLST import --force --no-prompt
+	#if $mlst
+	  -m $mlst
+	#end if
+	$database '$search' &amp;> $logfile
+  </command>
+  <inputs>
+	<param name="search" type="text" value="" optional="false" size="50"
+		   label="Species name to import"
+		   help="Bacterial species to download from pubMLST database" />
+	<param name="mlst" type="text" value="" optional="true" size="50"
+		   label="MLST shema"
+		   help="Precise mlst shema if multiple exists for the " />
+  </inputs>
+  <outputs>
+    <data name="logfile" format="txt" label="${tool.name} import on ${search}: log" />
+    <data name="database" format="sqlite" label="claMLST database on ${search}" />
+  </outputs>
+  <tests>
+	<test expect_num_outputs="2">
+      <param name="search" value="Escherichia spp" />
+      <param name="mlst" value="achtman" />
+      <output name="logfile" ftype="txt">
+		<assert_contents>
+		  <has_text text="One element found : escherichia spp" />
+		  <has_text text="One element found : mlst (achtman)" />
+		  <has_text text="Database initialized" />
+		</assert_contents>
+	  </output>
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+Import a classical MLST database from pubMLST
+Example :
+- Pseudomonas aeruginosa
+- Escherichia spp (mlst=achtman)
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
+  </help>
+  <citations>
+  </citations>
+</tool>