|
0
|
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 </help>
|
|
|
58 </tool> |
