diff wgmlst_export.xml @ 1:5b2c48fa0175 draft

planemo upload for repository https://github.com/bvalot/pyMLST commit fe04f6232a5f7ea78b666cb8036872902e79998b

--- a/wgmlst_export.xml	Thu Jun 16 12:32:28 2022 +0000
+++ b/wgmlst_export.xml	Wed Dec 07 15:25:06 2022 +0000
@@ -1,8 +1,10 @@
-<tool id="wgmlst_export_wrapper" name="Export result of cg/wgMLST database" version="2.1.3">
+<tool id="wgmlst_export_wrapper" name="Export result of cg/wgMLST database"
+	  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
   <description></description>
-  <requirements>
-	<requirement type="package" version="2.1.3">pymlst</requirement>
-  </requirements>
+  <macros>
+    <import>macro.xml</import>
+  </macros>
+  <expand macro="requirements" />
   <stdio>
     <exit_code range="1:" level="fatal" />
   </stdio>
@@ -14,6 +16,9 @@
 	#end if
 	#if $export_result.export == "mlst"
 	  mlst
+	  #if $export_result.mlsttype == "grapetree"
+	  -f grapetree
+	  #end if
 	#end if
 	#if $export_result.export == "strain"
 	  strain
@@ -49,7 +54,7 @@
            help="Sqlite format from cg/wgMLST database" />
 	<conditional name="export_result">
       <param name="export" type="select" label="Select the data export">
-		<option value="distance">Distance matrix between strains on the cg/wgMLST database</option>
+		<option value="distance" selected="true">Distance matrix between strains on the cg/wgMLST database</option>
 		<option value="mlst">cg/wgMLST table for each strain on the cg/wgMLST database</option>
 		<option value="strain">List of the strains on the cg/wgMLST database</option>
 		<option value="gene">List of the genes on the cg/wgMLST database</option>
@@ -59,7 +64,13 @@
                label="Report the number of gene found for each strain" />
       </when>
 	  <when value="distance" />
-	  <when value="mlst" />
+	  <when value="mlst">
+		<param name="mlsttype" type="select"
+			   label="Select the format of export">
+		  <option value="default" selected="true">Default format</option>
+		  <option value="grapetree">Grapetree format</option>
+		</param>
+	  </when>
 	  <when value="gene" />
 	</conditional>
 	<param name="mincover" type="integer" value="0"