<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>