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annotate emboss_epestfind.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: epestfind29" name="epestfind" version="5.0.0">
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2 <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
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5 -invalid $invalid -map $map -graph png -auto</command>
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6 <inputs>
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7 <param format="data" 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="window" type="text" value="10">
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11 <label>Minimal distance between positively charged amino acids</label>
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12 </param>
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13 <param name="order" type="select">
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14 <label>Sort by</label>
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15 <option value="3">Score</option>
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16 <option value="1">Length</option>
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17 <option value="2">Position</option>
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18 </param>
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19 <param name="threshold" type="text" value="5.0">
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20 <label>Threshold value to discriminate weak from potential PEST motifs.</label>
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21 </param>
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22 <param name="potential" type="select">
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23 <label>Decide whether potential PEST motifs should be printed</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 <param name="poor" type="select">
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28 <label>Decide whether poor PEST motifs should be printed</label>
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29 <option value="yes">Yes</option>
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30 <option value="no">No</option>
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31 </param>
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32 <param name="invalid" type="select">
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33 <label>Decide whether invalid PEST motifs should be printed</label>
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34 <option value="no">No</option>
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35 <option value="yes">Yes</option>
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36 </param>
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37 <param name="map" type="select">
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38 <label>Decide whether PEST motifs should be mapped to sequence</label>
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39 <option value="yes">Yes</option>
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40 <option value="no">No</option>
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41 </param>
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42 </inputs>
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43 <outputs>
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44 <data format="png" name="ofile2" />
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45 <data format="epestfind" name="ofile1" />
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46 </outputs>
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47 <!-- <tests>
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48 <test>
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49 <param name="input1" value="2.fasta"/>
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50 <param name="window" value="10"/>
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51 <param name="order" value="3"/>
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52 <param name="threshold" value="5.0"/>
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53 <param name="potential" value="yes"/>
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54 <param name="poor" value="yes"/>
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55 <param name="invalid" value="no"/>
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56 <param name="map" value="yes"/>
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57 <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
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58 </test>
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59 </tests> output file contains file location info -->
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60 <help>
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61 You can view the original documentation here_.
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62
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63 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html
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64
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65 ------
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66
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67 **Citation**
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68
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69 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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70
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71 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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72 </help>
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73 </tool>