<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>