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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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1 <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
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2 <description>Finds DNA inverted repeats</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -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>On query</label>
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8 </param>
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9 <param name="gap" type="text" value="12">
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10 <label>Gap penalty</label>
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11 </param>
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12 <param name="threshold" type="text" value="50">
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13 <label>Minimum score threshold</label>
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14 </param>
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15 <param name="match" type="text" value="3">
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16 <label>Match score</label>
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17 </param>
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18 <param name="mismatch" type="text" value="-4">
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19 <label>Mismatch score</label>
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20 </param>
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21 <param name="maxrepeat" type="text" value="2000">
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22 <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
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23 </param>
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24 </inputs>
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25 <outputs>
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26 <data format="einverted" name="out_file1" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input1" value="1.fasta"/>
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31 <param name="gap" value="12"/>
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32 <param name="threshold" value="50"/>
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33 <param name="match" value="3"/>
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34 <param name="mismatch" value="-4"/>
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35 <param name="maxrepeat" value="2000"/>
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36 <output name="out_file1" file="emboss_einverted_out.einverted"/>
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37 </test>
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38 </tests>
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39 <help>
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40 .. class:: warningmark
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41
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42 The input dataset needs to be sequences.
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43
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44 -----
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45
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46 You can view the original documentation here_.
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47
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48 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html
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49
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50 ------
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51
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52 **Citation**
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53
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54 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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55
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56 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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57 </help>
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58 </tool>