annotate tools/emboss_5/emboss_textsearch.xml @ 0:9071e359b9a3

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<tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0">
  <description>Search sequence documentation. Slow, use SRS and Entrez!</description>
  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
  <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 format="data" name="input1" type="data">
      <label>Sequence</label>
    </param>
    <param name="pattern" size="50" type="text" value="">
      <label>Pattern to search for</label>
    </param>
    <param name="casesensitive" type="select">
      <label>Do a case-sensitive search</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
    <param name="heading" type="select">
      <label>Display column headings</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="usa" type="select">
      <label>Display the USA of the sequence</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="accession" type="select">
      <label>Display accession column</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="search_name" type="select">
      <label>Display name column</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="description" type="select">
      <label>Display description column</label>
      <option value="yes">Yes</option>
      <option value="no">No</option>
    </param>
    <param name="html_out1" type="select">
      <label>Format output as an HTML table</label>
      <option value="no">No</option>
      <option value="yes">Yes</option>
    </param>
  </inputs>
  <outputs>
    <data format="textsearch" name="out_file1" />
  </outputs>
  <code file="emboss_format_corrector.py" />
  <help>
    You can view the original documentation here_.
    
    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html
  </help>
</tool>