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annotate emboss_newcpgseek.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: newcpgseek58" name="newcpgseek" version="5.0.0">
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2 <description>Reports CpG rich region</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>newcpgseek -sequence $input1 -outfile $out_file1 -score $score -auto</command>
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5 <inputs>
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6 <param format="fasta" name="input1" type="data">
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7 <label>Sequence</label>
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8 </param>
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9 <param name="score" type="text" value="17">
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10 <label>CpG score</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="newcpgseek" name="out_file1" />
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="input1" value="2.fasta"/>
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19 <param name="score" value="17"/>
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20 <output name="out_file1" file="emboss_newcpgseek_out.newcpgseek"/>
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21 </test>
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22 </tests>
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23 <help>
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25 .. class:: warningmark
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27 The input dataset needs to be sequences.
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29 -----
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9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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31 You can view the original documentation here_.
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33 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgseek.html
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35 ------
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37 **Citation**
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39 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 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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42 </help>
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43 </tool>