view emboss_palindrome.xml @ 19:d0847fe9b443 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"

<tool id="EMBOSS: palindrome65" name="palindrome" version="@VERSION@.1">
  <description>Looks for inverted repeats in a nucleotide sequence</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>palindrome -sequence '$input1' -outfile '$out_file1' -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
  <inputs>
    <param name="input1" type="data" format="fasta" label="Sequences" />
    <param name="minpallen" type="integer" value="10" label="Minimum length of palindrome" />
    <param name="maxpallen" type="integer" value="100" label="Maximum length of palindrome" />
    <param name="gaplimit" type="integer" value="100" label="Maximum gap between repeated regions" />
    <param name="nummismatches" type="integer" value="0" label="Number of mismatches allowed" />
    <param name="overlap" type="select" label="Report overlapping matches">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="palindrome" />
  </outputs>
  <tests>
    <test>
      <param name="input1" value="2.fasta"/>
      <param name="minpallen" value="10"/>
      <param name="maxpallen" value="100"/>
      <param name="gaplimit" value="100"/>
      <param name="nummismatches" value="0"/>
      <param name="overlap" value="yes"/>
      <output name="out_file1" file="emboss_palindrome_out.palindrome"/>
    </test>
  </tests>
  <help>
.. class:: warningmark

The input dataset needs to be sequences.

-----

    You can view the original documentation here_.

    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/palindrome.html
  </help>
  <expand macro="citations" />
</tool>