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annotate emboss_etandem.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: etandem33" name="etandem" version="5.0.0">
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2 <description>Looks for tandem repeats in a nucleotide sequence</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
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5 <inputs>
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6 <param format="fasta" 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="minrepeat" type="text" value="10">
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10 <label>Minimum repeat size</label>
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11 </param>
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12 <param name="maxrepeat" type="text" value="10">
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13 <label>Maximum repeat size</label>
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14 </param>
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15 <param name="threshold" type="text" value="20">
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16 <label>Threshold score</label>
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17 </param>
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18 <param name="mismatch" type="select">
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19 <label>Allow N as a mismatch</label>
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20 <option value="no">No</option>
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21 <option value="yes">Yes</option>
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22 </param>
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23 <param name="uniform" type="select">
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24 <label>Allow uniform consensus</label>
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25 <option value="no">No</option>
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26 <option value="yes">Yes</option>
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27 </param>
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28 <param name="out_format1" type="select">
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29 <label>Output Report File Format</label>
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30 <option value="table">Table</option>
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31 <option value="embl">EMBL</option>
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32 <option value="genbank">GENBANK</option>
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33 <option value="gff">GFF</option>
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34 <option value="pir">PIR</option>
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35 <option value="swiss">SwissProt</option>
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36 <option value="dbmotif">DbMotif</option>
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37 <option value="diffseq">Diffseq</option>
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38 <option value="excel">Excel (tab delimited)</option>
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39 <option value="feattable">FeatTable</option>
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40 <option value="motif">Motif</option>
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41 <option value="regions">Regions</option>
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42 <option value="seqtable">SeqTable</option>
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43 <option value="simple">SRS Simple</option>
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44 <option value="srs">SRS</option>
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45 <option value="tagseq">TagSeq</option>
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46 </param>
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47 </inputs>
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48 <outputs>
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49 <data format="etandem" name="out_file1" />
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50 <data format="table" name="ofile2" />
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="input1" value="1.fasta"/>
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55 <param name="minrepeat" value="10"/>
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56 <param name="maxrepeat" value="10"/>
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57 <param name="threshold" value="20"/>
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58 <param name="mismatch" value="no"/>
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59 <param name="uniform" value="no"/>
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60 <param name="out_format1" value="table"/>
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61 <output name="ofile2" file="emboss_etandem_out.table"/>
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62 </test>
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63 </tests>
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64 <code file="emboss_format_corrector.py" />
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65 <help>
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66 .. class:: warningmark
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67
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68 The input dataset needs to be sequences.
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69
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70 -----
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71
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72 You can view the original documentation here_.
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73
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74 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/etandem.html
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75
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76 ------
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77
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78 **Citation**
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79
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80 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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81
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82 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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83 </help>
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84 </tool>
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86