--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wgmlst_remove.xml	Wed Dec 07 15:25:06 2022 +0000
@@ -0,0 +1,118 @@
+<tool id="wgmlst_remove_wrapper"
+	  name="Remove strain/gene to cg/wgMLST database"
+	  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+  <description></description>
+  <macros>
+    <import>macro.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+  <version_command>wgMLST -v</version_command>
+  <command><![CDATA[
+	cp '${database}' '${databaseout}' && wgMLST remove 
+	#if $element == "strain"
+	  --strains
+	#else 
+	  --genes
+	#end if
+	#if $data.input == "textinput"
+	  '${databaseout}' 
+	  #for $strain in $data.textelement.split(" ")
+	    '$strain'
+	  #end for
+	#else
+	  -f '${data.fileelement}' '${databaseout}'
+	#end if
+	#if $log
+	  2> '${logfile}'
+	#end if
+	]]>
+  </command>
+  <inputs>
+	<param name="database" type="data"
+           format="sqlite"
+           label="cg/wgMLST database"
+           help="Sqlite format from cg/wgMLST database" />
+	<param name="element" type="select" label="Select type of data to remove">
+        <option value="strain" selected="true">Strain(s)</option>
+        <option value="gene">Gene(s)</option>
+	  </param>
+	<conditional name="data">
+	  <param name="input" type="select" label="Select source of data">
+        <option value="textinput" selected="true">List elements manually</option>
+        <option value="fileinput">List elements from file</option>
+	  </param>
+	  <when value="textinput">
+		<param name="textelement" type="text" value="" optional="false" size="50"
+               label="Name of strain/gene to removed from database"
+               help="Separated each strain/gene by a space and quote it"/>
+      </when>	  
+	  <when value="fileinput">
+        <param name="fileelement" type="data" format="txt"
+               label="File list of strain/gene to removed"
+			   help="txt format" />
+      </when>	
+	</conditional>
+	<param name="log" type="boolean" checked="true"
+           label="Write log file" />
+  </inputs>
+  <outputs>
+    <data name="databaseout" format="sqlite" label="${database.name}">
+	</data>
+    <data name="logfile" format="txt" label="${tool.name} on ${database.name}: log">
+	  <filter>log</filter>
+	</data>	
+  </outputs>
+  <tests>
+	<test expect_num_outputs="2">
+	  <param name="database" value="wgmlst_ecoli.db" />
+	  <param name="element" value="strain" />	  
+	  <conditional name="data">
+		<param name="input" value="textinput" />
+		<param name="textelement" value="EEES_003 EEES_004" />
+	  </conditional>
+	  <output name="logfile" ftype="txt">
+	  <assert_contents>
+		<has_text text="EEES_004 : OK" />
+		<has_text text="EEES_003 : OK" />
+	  </assert_contents>
+	  </output>
+	</test>
+	<test expect_num_outputs="2">
+	  <param name="database" value="wgmlst_ecoli.db" />
+	  <param name="element" value="gene" />	  
+	  <conditional name="data">
+		<param name="input" value="fileinput" />
+		<param name="fileelement" ftype="txt" value="wgmlst_ecoli.db.gene_to_removed" />
+	  </conditional>
+	  <output name="logfile" ftype="txt">
+	  <assert_contents>
+		<has_text text="b0004 : OK" />
+		<has_text text="C-RS24040 : OK" />
+		<has_text text="ECs4518 : OK" />
+	  </assert_contents>
+	  </output>
+	</test>
+  </tests>
+  <help>
+**What it does**
+
+Remove STRAINS or GENES from a cg/wgMLST DATABASE.
+
+You can indicated the STRAIN or GENE to remove:
+ - Typing element separated by space
+ - Using a file containing these elements
+
+**Options:**
+  --strains / --genes  Choose the item you wish to remove
+  -f, --file FILENAME  File list of genes or strains to removed on the wgMLST database.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
+  </help>
+  <citations>
+  </citations>
+</tool>