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/tools/emboss_5/emboss_textsearch.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="EMBOSS: textsearch98" name="textsearch" version="5.0.0">
 2  <description>Search sequence documentation. Slow, use SRS and Entrez!</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html
 5  $html_out1 -auto</command>
 6  <inputs>
 7    <param format="data" name="input1" type="data">
 8      <label>Sequence</label>
 9    </param>
10    <param name="pattern" size="50" type="text" value="">
11      <label>Pattern to search for</label>
12    </param>
13    <param name="casesensitive" type="select">
14      <label>Do a case-sensitive search</label>
15      <option value="no">No</option>
16      <option value="yes">Yes</option>
17    </param>
18    <param name="heading" type="select">
19      <label>Display column headings</label>
20      <option value="yes">Yes</option>
21      <option value="no">No</option>
22    </param>
23    <param name="usa" type="select">
24      <label>Display the USA of the sequence</label>
25      <option value="yes">Yes</option>
26      <option value="no">No</option>
27    </param>
28    <param name="accession" type="select">
29      <label>Display accession column</label>
30      <option value="yes">Yes</option>
31      <option value="no">No</option>
32    </param>
33    <param name="search_name" type="select">
34      <label>Display name column</label>
35      <option value="yes">Yes</option>
36      <option value="no">No</option>
37    </param>
38    <param name="description" type="select">
39      <label>Display description column</label>
40      <option value="yes">Yes</option>
41      <option value="no">No</option>
42    </param>
43    <param name="html_out1" type="select">
44      <label>Format output as an HTML table</label>
45      <option value="no">No</option>
46      <option value="yes">Yes</option>
47    </param>
48  </inputs>
49  <outputs>
50    <data format="textsearch" name="out_file1" />
51  </outputs>
52  <code file="emboss_format_corrector.py" />
53  <help>
54    You can view the original documentation here_.
55    
56    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html
57
58------
59
60**Citation**
61
62If 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;`_
63  </help>
64</tool>