<tool id="wgmlst_sequence_wrapper" name="Sequences of 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 sequence
	#if str($genes)
	  -f '${genes}'
	#end if
	#if $reference
	  --reference
	#end if
	'${database}' > '${sequence}'
	#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="genes" type="data"
           format="txt"
           label="Genes list"
           help="File containing list of genes to extract" />
	<param name="reference" type="boolean" checked="false"
           label="Report the number of gene found for each strain" />
	<param name="log" type="boolean" checked="false"
           label="Write log file" /> 
  </inputs>
  <outputs>
    <data name="logfile" format="txt" label="Sequence of
											 ${database.name}: log">
	  <filter>log</filter>
	</data>
	<data name="sequence" format="fasta" label="Sequence of ${database.name}: fasta" />
  </outputs>
  <tests>
	<test expect_num_outputs="1">
      <param name="database" value="wgmlst_ecoli.db" />
	  <param name="genes" value="wgmlst_ecoli.db.gene" />
	  <param name="reference" value="true" />
      <output name="sequence" ftype="fasta" file="wgmlst_ecoli.db.sequence" />
    </test>
  </tests>
  <help>
**What it does**

Extract sequences from a wgMLST DATABASE.

**Options**

  -f, --file FILENAME    File containing list of coregenes to extract
                         (default:all coregenes).
  --reference            Return sequence of the reference instead of
                         strains allele

**License and citation**

This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`.
  </help>
  <citations>
  </citations>
</tool>