comparison emboss_textsearch.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

10:9b98d3d903c6

<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" 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

------

**Citation**

For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_

If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
  </help>
</tool>

11:0e2484b6829b

<tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0">
  <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>