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annotate emboss_palindrome.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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1 <tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0">
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2 <description>Looks for inverted repeats in a nucleotide sequence</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
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5 <inputs>
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6 <param format="fasta" name="input1" type="data">
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7 <label>Sequences</label>
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8 </param>
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9 <param name="minpallen" type="text" value="10">
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10 <label>Minimum length of palindrome</label>
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11 </param>
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12 <param name="maxpallen" type="text" value="100">
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13 <label>Maximum length of palindrome</label>
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14 </param>
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15 <param name="gaplimit" type="text" value="100">
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16 <label>Maximum gap between repeated regions</label>
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17 </param>
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18 <param name="nummismatches" type="text" value="0">
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19 <label>Number of mismatches allowed</label>
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20 </param>
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21 <param name="overlap" type="select">
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22 <label>Report overlapping matches</label>
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23 <option value="yes">Yes</option>
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24 <option value="no">No</option>
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25 </param>
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26 </inputs>
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27 <outputs>
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28 <data format="palindrome" name="out_file1" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input1" value="2.fasta"/>
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33 <param name="minpallen" value="10"/>
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34 <param name="maxpallen" value="100"/>
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35 <param name="gaplimit" value="100"/>
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36 <param name="nummismatches" value="0"/>
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37 <param name="overlap" value="yes"/>
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38 <output name="out_file1" file="emboss_palindrome_out.palindrome"/>
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39 </test>
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40 </tests>
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41 <help>
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42
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43 .. class:: warningmark
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44
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45 The input dataset needs to be sequences.
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46
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47 -----
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48
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49 You can view the original documentation here_.
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50
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51 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.html
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52
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53 ------
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54
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55 **Citation**
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56
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57 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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58
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59 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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60 </help>
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61 </tool>