<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="0.9.0">
  <description>with header satisfying a query string</description>
  <command interpreter="python">cherry_pick-fasta.py
                                   --input "$input"
                                   --query-string $query
                                   --output $output
  </command>

  <inputs>
    <param name="query" type="text" size="30" value="" label="Select sequences with this string in their header" help="exemple:'gi|40557596'">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="&quot;"/>
          <remove value="\"/>
        </valid>
        <mapping initial="none">
          <add source="&quot;" target="\&quot;"/>
          <add source="\" target="\\"/>
        </mapping>
      </sanitizer>
    </param>
    <param format="fasta" label="Source file" name="input" type="data" />
  </inputs>
  <outputs>
    <data name="output" format="fasta" label="${tool.name} on ${input.value} with query: ${query.value}" />
  </outputs>
  <tests>
    <test>
        <param ftype="fasta" name="input" value="input.fa" />
        <param name="query" value="AAR88092.1" />
        <output name="output" ftype="fasta" file="output.fa" />
    </test>
  </tests>
  <help>
**What it does**

This tool retrieves nucleotide/peptide sequences from a fasta file whose headers match a given query string

It is Copyright © 2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_.

.. _MIT license: http://opensource.org/licenses/MIT

  </help>
  <citations>
      <citation></citation>
  </citations>
</tool>