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