view emboss_textsearch.xml @ 19:d0847fe9b443 draft

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

<tool id="EMBOSS: textsearch98" name="textsearch" version="@VERSION@">
  <description>Search sequence documentation. Slow, use SRS and Entrez!</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <code file="emboss_format_corrector.py" />
  <command>textsearch -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html
  $html_out1 -auto</command>
  <inputs>
    <param name="input1" type="data" format="data" label="Sequence" />
    <param name="pattern" type="text" value="" label="Pattern to search for" />
    <param name="casesensitive" type="select" label="Do a case-sensitive search">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="heading" type="select" label="Display column headings">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="usa" type="select" label="Display the USA of the sequence">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="accession" type="select" label="Display accession column">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="search_name" type="select" label="Display name column">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="description" type="select" label="Display description column">
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="html_out1" type="select" label="Format output as an HTML table">
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data name="out_file1" format="textsearch" />
  </outputs>
  <help>
    You can view the original documentation here_.

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