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annotate emboss_plotorf.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: plotorf76" name="plotorf" version="5.0.0">
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2 <!-- produces png file output -->
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3 <description>Plot potential open reading frames</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 plotorf -sequence $input1 -graph png -goutfile $out_file1 -start $start -stop $stop -auto</command>
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6 <inputs>
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7 <param format="fasta" name="input1" type="data">
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8 <label>Sequence</label>
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9 </param>
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10 <param name="start" type="text" value="ATG">
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11 <label>Start codons</label>
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12 </param>
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13 <param name="stop" type="text" value="TAA">
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14 <label>Stop codons</label>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data format="png" name="out_file1" />
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19 </outputs>
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20 <!-- <tests>
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21 <test>
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22 <param name="input1" value="2.fasta"/>
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23 <param name="start" value="ATG"/>
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24 <param name="stop" value="TAA"/>
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25 <output name="out_file1" file="emboss_plotorf_out.png"/>
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26 </test>
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27 </tests> -->
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28 <help>
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29
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30 .. class:: warningmark
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32 The input dataset needs to be sequences.
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34 -----
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36 You can view the original documentation here_.
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38 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotorf.html
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40 ------
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42 **Citation**
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44 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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46 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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47 </help>
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48 </tool>