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annotate emboss_pepcoil.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: pepcoil68" name="pepcoil" version="5.0.0">
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2 <description>Predicts coiled coil regions</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>pepcoil -sequence $input1 -outfile $out_file1 -window $window -coil $coil -frame $frame -other $other -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="28">
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10 <label>Window size</label>
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11 </param>
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12 <param name="coil" type="select">
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13 <label>Report coiled coil regions</label>
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14 <option value="yes">Yes</option>
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15 <option value="no">No</option>
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16 </param>
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17 <param name="frame" type="select">
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18 <label>Show coil frameshifts</label>
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19 <option value="yes">Yes</option>
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20 <option value="no">No</option>
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21 </param>
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22 <param name="other" type="select">
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23 <label>Report non coiled coil regions</label>
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24 <option value="yes">Yes</option>
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25 <option value="no">No</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="pepcoil" name="out_file1" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input1" value="2.fasta"/>
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34 <param name="window" value="28"/>
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35 <param name="coil" value="yes"/>
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36 <param name="frame" value="yes"/>
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37 <param name="other" value="yes"/>
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38 <output name="out_file1" file="emboss_pepcoil_out.pepcoil"/>
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39 </test>
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40 </tests>
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41 <help>
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42 You can view the original documentation here_.
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43
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44 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepcoil.html
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45
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46 ------
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47
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48 **Citation**
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49
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50 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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51
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52 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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53 </help>
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54 </tool>