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annotate emboss_textsearch.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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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" 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
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58 ------
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59
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60 **Citation**
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61
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62 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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63
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64 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
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65 </help>
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66 </tool>