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annotate emboss_wordmatch.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: wordmatch110" name="wordmatch" version="5.0.0">
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2 <description>Finds all exact matches of a given size between 2 sequences</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2
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5 -offormat5 $out_format3 -auto</command>
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6 <inputs>
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7 <param format="fasta" 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="fasta" 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="4">
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14 <label>Word size</label>
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15 </param>
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16 <param name="out_format1" type="select">
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17 <label>Output Alignment File Format</label>
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18 <option value="match">Match (m)</option>
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19 <option value="simple">Simple (m)</option>
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20 <option value="fasta">FASTA (m)</option>
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21 <option value="msf">MSF (m)</option>
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22 <option value="srs">SRS (m)</option>
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23 <option value="pair">Pair (p)</option>
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24 <option value="markx0">Markx0 (p)</option>
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25 <option value="markx1">Markx1 (p)</option>
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26 <option value="markx2">Markx2 (p)</option>
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27 <option value="markx3">Markx3 (p)</option>
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28 <option value="markx10">Markx10 (p)</option>
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29 <option value="srspair">SRS pair (p)</option>
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30 <option value="score">Score (p)</option>
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31 </param>
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32 <param name="out_format2" type="select">
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33 <label>Output Feature 1 File Format</label>
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34 <option value="gff">GFF</option>
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35 <option value="embl">EMBL</option>
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36 <option value="swiss">SwissProt</option>
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37 </param>
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38 <param name="out_format3" type="select">
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39 <label>Output Feature 2 File Format</label>
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40 <option value="gff">GFF</option>
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41 <option value="embl">EMBL</option>
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42 <option value="swiss">SwissProt</option>
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43 </param>
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44 </inputs>
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45 <outputs>
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46 <data format="match" name="out_file1" />
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47 <data format="gff" name="out_file2" />
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48 <data format="gff" name="out_file3" />
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49 </outputs>
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50 <!-- <tests>
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51 <test>
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52 <param name="input1" value="2.fasta"/>
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53 <param name="input2" value="1.fasta"/>
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54 <param name="wordsize" value="4"/>
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55 <param name="out_format1" value="fasta"/>
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56 <param name="out_format2" value="gff"/>
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57 <param name="out_format3" value="gff"/>
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58 <output name="ofile2" file="emboss_wordmatch_out.embl"/>
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59 </test>
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60 </tests> test takes a long time to run-->
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61 <code file="emboss_format_corrector.py" />
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62 <help>
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63
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64 .. class:: warningmark
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65
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66 The input datasets need to be sequences.
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67
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68 -----
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69
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70 You can view the original documentation here_.
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71
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72 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html
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73
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74 ------
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75
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76 **Citation**
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77
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78 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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79
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80 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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81 </help>
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82 </tool>