Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_textsearch.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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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 </help> | |
| 58 </tool> |