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annotate emboss_dreg.xml @ 10:9b98d3d903c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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1 <tool id="EMBOSS: dreg27" name="dreg" version="5.0.0">
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2 <description>Regular expression search of a nucleotide sequence</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto</command>
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5 <inputs>
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6 <param format="data" name="input1" type="data">
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7 <label>Sequence 1</label>
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8 </param>
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9 <param name="pattern" type="text" value="(AUG)">
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10 <label>Regular expression pattern</label>
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11 </param>
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12 </inputs>
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13 <outputs>
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14 <data format="dreg" name="out_file1" />
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15 </outputs>
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16 <!-- tests not possible since dreg timestamps output file -->
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17 <help>
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18 You can view the original documentation here_.
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20 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dreg.html
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22 ------
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24 **Citation**
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26 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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28 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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29 </help>
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30 </tool>