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annotate emboss_newcpgreport.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: newcpgreport57" name="newcpgreport" version="5.0.0">
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2 <description>Report CpG rich areas</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -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</label>
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8 </param>
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9 <param name="window" type="text" value="100">
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10 <label>Window Size</label>
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11 </param>
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12 <param name="shift" type="text" value="1">
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13 <label>Step size (shift)</label>
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14 </param>
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15 <param name="minlen" type="text" value="200">
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16 <label>Minimum length</label>
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17 </param>
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18 <param name="minoe" type="text" value="0.6">
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19 <label>Minimum average observed to expected ratio</label>
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20 </param>
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21 <param name="minpc" type="text" value="50.0">
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22 <label>Minimum average percentage of G plus C</label>
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23 </param>
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24 </inputs>
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25 <outputs>
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26 <data format="newcpgreport" name="out_file1" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input1" value="2.fasta"/>
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31 <param name="window" value="100"/>
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32 <param name="shift" value="1"/>
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33 <param name="minlen" value="200"/>
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34 <param name="minoe" value="0.6"/>
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35 <param name="minpc" value="50.0"/>
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36 <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/>
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37 </test>
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38 </tests>
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39 <help>
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40 You can view the original documentation here_.
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41
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42 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html
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43
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44 ------
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45
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46 **Citation**
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47
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48 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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49
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50 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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51 </help>
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52 </tool>