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annotate emboss_polydot.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: polydot77" name="polydot" version="5.0.0">
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2 <!-- produces png file, not added functional tests -->
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3 <description>Displays all-against-all dotplots of a set of sequences</description>
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4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap
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6 $gap -auto</command>
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7 <inputs>
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8 <param format="fasta" name="input1" type="data">
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9 <label>Sequence</label>
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10 </param>
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11 <param name="wordsize" type="text" value="6">
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12 <label>Word size</label>
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13 </param>
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14 <param name="boxit" type="select">
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15 <label>Draw a box around each dotplot</label>
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16 <option value="yes">Yes</option>
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17 <option value="no">No</option>
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18 </param>
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19 <param name="gap" type="text" value="10">
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20 <label>Size of gap</label>
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data format="polydot" name="output1" />
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25 <data format="png" name="output2" />
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26 </outputs>
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27 <!-- <tests>
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28 <test>
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29 <param name="input1" value="2.fasta"/>
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30 <param name="wordsize" value="6"/>
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31 <param name="boxit" value="yes"/>
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32 <param name="gap" value="10"/>
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33 <output name="output1" file="emboss_polydot_out.png"/>
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34 </test>
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35 </tests>-->
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36 <help>
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37
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38 .. class:: warningmark
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39
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40 The input dataset needs to be sequences.
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41
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42 -----
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43
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44 You can view the original documentation here_.
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45
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46 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/polydot.html
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47
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48 ------
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49
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50 **Citation**
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51
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52 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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53
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54 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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55 </help>
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56 </tool>