view cherry_pick_fasta.xml @ 0:e3aee4ba49c6 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3

<tool id="cherry_pick_fasta" name="Pick Fasta sequences" version="1.0.0">
  <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 ${on_string} including '${query.value}' in header" />
  </outputs>
  <tests>
    <test>
        <param ftype="fasta" name="input" value="input.fa" />
        <param name="query" value="gi|81971654" />
        <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`_.

.. _CNRS and University Pierre et Marie Curie: http://www.upmc.fr/en/index.html
.. _MIT license: http://opensource.org/licenses/MIT

  </help>
</tool>