--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wgmlst_create.xml	Thu Jun 16 12:32:28 2022 +0000
@@ -0,0 +1,59 @@
+<tool id="wgmlst_create_wrapper" name="Create cg/wgMLST 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>wgMLST -v</version_command>
+  <command>
+    wgMLST create --force 
+	#if $concatenate
+	  -c 
+	#end if
+	#if $remove
+	  -r 
+	#end if
+	'${database}' '${coregene}' &amp;> '${logfile}'
+  </command>
+  <inputs>
+	<param name="coregene" type="data" format="fasta"
+           label="Multiple fasta with GENES sequence" help="Fasta format" />
+	<param name="concatenate" type="boolean" checked="false"
+           label="Automatically concatenate GENES with duplicated sequences" />
+	<param name="remove" type="boolean" checked="false"
+           label="Automatically remove GENES with duplicated sequences" />
+  </inputs>
+  <outputs>
+    <data name="logfile" format="txt" label="${tool.name} on ${coregene.name}: log" />
+    <data name="database" format="sqlite" label="cg/wgMLST database on ${coregene.name}" />
+  </outputs>
+  <tests>
+	<test expect_num_outputs="2">
+      <param name="coregene" ftype="fasta" value="EHSB-021_gene.fasta" />
+	  <param name="remove" value="true" />
+      <output name="logfile" ftype="txt">
+		<assert_contents>
+		  <has_text text="Skipped invalid genes: 99" />
+		  <has_text text="Database initialized" />
+		</assert_contents>
+	  </output>
+    </test>
+  </tests>
+  <help>
+**What it does**
+
+Create a cg/wgMLST DATABASE from a template COREGENE.
+
+Options:
+  -c, --concatenate  Automatically concatenate GENES with duplicated sequences.
+  -r, --remove       Automatically remove GENES with duplicated sequences.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
+  </help>
+  <citations>
+  </citations>
+</tool>