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annotate emboss_octanol.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: octanol63" name="octanol" version="5.0.0">
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2 <!-- graphics output with filename, no functional tests added -->
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3 <description>Displays protein hydropathy</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 octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot
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6 -differenceplot $differenceplot -auto</command>
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7 <inputs>
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8 <param format="data" name="input1" type="data">
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9 <label>Sequences</label>
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10 </param>
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11 <param name="width" type="text" value="19">
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12 <label>Window size</label>
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13 </param>
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14 <param name="octanolplot" type="select">
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15 <label>Display the octanol plot</label>
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16 <option value="no">No</option>
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17 <option value="yes">Yes</option>
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18 </param>
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19 <param name="interfaceplot" type="select">
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20 <label>Display the interface plot</label>
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21 <option value="no">No</option>
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22 <option value="yes">Yes</option>
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23 </param>
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24 <param name="differenceplot" type="select">
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25 <label>Display the difference plot</label>
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26 <option value="yes">Yes</option>
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27 <option value="no">No</option>
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28 </param>
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29 </inputs>
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30 <outputs>
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31 <data format="png" name="out_file1" />
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32 </outputs>
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33 <help>
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34 You can view the original documentation here_.
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35
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36 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/octanol.html
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37
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38 ------
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39
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40 **Citation**
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41
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42 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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43
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44 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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45 </help>
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46 </tool>