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1 <tool id="EMBOSS: dotpath25" name="dotpath" version="5.0.0">
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2 <description>Non-overlapping wordmatch dotplot of two sequences</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png
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5 -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 1</label>
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9 </param>
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10 <param format="data" name="input2" type="data">
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11 <label>Sequence 2</label>
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12 </param>
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13 <param name="wordsize" size="4" type="text" value="4">
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14 <label>Word size (Integer 2 or more)</label>
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15 </param>
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16 <param name="overlaps" type="select">
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17 <label>Display the overlapping matches (in red) as well as the minimal set of non-overlapping matches</label>
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18 <option value="no">No</option>
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19 <option value="yes">Yes</option>
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20 </param>
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21 <param name="boxit" type="select">
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22 <label>Draw a box around dotplot</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="png" name="out_file1" />
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29 </outputs>
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30 <!-- functional tests not possible since image output contains file name information and timestamp -->
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31 <help>
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32 You can view the original documentation here_.
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33
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34 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotpath.html
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35 </help>
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36 </tool> |
