/tools/emboss_5/emboss_textsearch.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 64 lines · 60 code · 4 blank · 0 comment · 0 complexity · 680bfe046d77e4a400e1296b24b3a6fb MD5 · raw file
- <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" size="50" 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**
-
- 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_
- </help>
- </tool>