view emboss_dreg.xml @ 19:d0847fe9b443 draft

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

<tool id="EMBOSS: dreg27" name="dreg" version="@VERSION@+galaxy1">
  <description>Regular expression search of a nucleotide sequence</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>dreg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence 1" />
    <param name="pattern" type="text" value="(AUG)" label="Regular expression pattern">
      <expand macro="regex_sanitizer"/>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="dreg" />
  </outputs>
  <tests>
    <test>
      <param name="input1" ftype="fasta" value="2.fasta"/>
      <param name="pattern" value="g[atcg]ctct{2,2}gcc"/>
      <output name="out_file1" value="dreg.seqtable" lines_diff="8"/>
    </test>
  </tests>
  <help>
    You can view the original documentation here_.

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