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annotate emboss_diffseq.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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1 <tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0">
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2 <description>Find differences between nearly identical sequences</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
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5 $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -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 1</label>
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9 </param>
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10 <param format="data" name="input2" type="data">
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11 <label>Sequence 2</label>
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12 </param>
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13 <param name="wordsize" type="text" value="20">
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14 <label>Wordsize</label>
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15 </param>
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16 <param name="globaldifferences" type="select">
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17 <label>Report differences at the ends</label>
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18 <option value="no">No</option>
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19 <option value="yes">Yes</option>
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20 </param>
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21 <param name="out_format1" type="select">
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22 <label>Output Report File Format</label>
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23 <option value="diffseq">Diffseq</option>
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24 <option value="embl">EMBL</option>
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25 <option value="genbank">GENBANK</option>
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26 <option value="gff">GFF</option>
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27 <option value="pir">PIR</option>
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28 <option value="swiss">SwissProt</option>
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29 <option value="dbmotif">DbMotif</option>
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30 <option value="excel">Excel (tab delimited)</option>
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31 <option value="feattable">FeatTable</option>
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32 <option value="motif">Motif</option>
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33 <option value="regions">Regions</option>
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34 <option value="seqtable">SeqTable</option>
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35 <option value="simple">SRS Simple</option>
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36 <option value="srs">SRS</option>
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37 <option value="table">Table</option>
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38 <option value="tagseq">TagSeq</option>
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39 </param>
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40 <param name="out_format2" type="select">
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41 <label>Sequence 1 Output Feature File Format</label>
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42 <option value="gff">GFF</option>
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43 <option value="embl">EMBL</option>
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44 <option value="swiss">SwissProt</option>
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45 </param>
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46 <param name="out_format3" type="select">
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47 <label>Sequence 2 Output Feature File Format</label>
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48 <option value="gff">GFF</option>
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49 <option value="embl">EMBL</option>
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50 <option value="swiss">SwissProt</option>
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51 </param>
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52 </inputs>
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53 <outputs>
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54 <data format="diffseq" name="out_file1" />
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55 <data format="gff" name="out_file2" />
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56 <data format="gff" name="out_file3" />
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57 </outputs>
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58 <code file="emboss_format_corrector.py" />
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59 <help>
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60 You can view the original documentation here_.
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61
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62 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html
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63
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64 ------
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65
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66 **Citation**
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67
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68 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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69
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70 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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71 </help>
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72 </tool>