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annotate emboss_dotpath.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: 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" 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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36 ------
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37
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38 **Citation**
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39
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40 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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41
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42 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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43 </help>
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44 </tool>