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1 <tool id="glimmer_not-knowlegde-based" name="Glimmer3" version="0.1">
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2 <description>Predict ORFs in prokaryotic genomes (not knowlegde-based)</description>
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3 <requirements>
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4 <requirement type="package" version="3.02b">glimmer</requirement>
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5 <requirement type="package" version="1.61">biopython</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 glimmer_wo_icm.py
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9 $input
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10 #if $report:
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11 $prediction
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12 #else:
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13 "None"
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14 #end if
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15 #if $detailed_report:
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16 $detailed
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17 #else:
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18 "None"
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19 #end if
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20 $overlap
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21 $gene_length
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22 $threshold
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23 $linear
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24 $genes_output
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25 </command>
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26 <inputs>
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27 <param name="input" type="data" format="fasta" label="Genome sequence" />
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28 <param name="overlap" type="integer" value="0" label="Set maximum overlap length. Overlaps this short or shorter are ignored." />
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29 <param name="gene_length" type="integer" value="110" label="Set minimum gene length." />
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30 <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene." />
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31 <param name="linear" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" />
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32
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33 <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file" />
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34 <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output" />
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35 </inputs>
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36 <outputs>
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37 <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
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38 <data name="prediction" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
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39 <filter>report == True</filter>
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40 </data>
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41 <data name="detailed" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
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42 <filter>detailed_report == True</filter>
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43 </data>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input" value="streptomyces_coelicolor.dna" />
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48 <output name="output" file="fasta_tool_convert_from_dna.out" />
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49 </test>
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50 </tests>
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51 <help>
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52
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53 **What it does**
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54
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55 This tool predicts open reading frames (orfs) from a given DNA Sequence. That tool is not knowlegde-based.
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56
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57 The recommended way is to use a trained Glimmer3 with ICM model. Use the knowlegde-based version for that and insert/generate a training set.
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58
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59 -----
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60
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61 **Example**
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62
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63 Suppose you have the following DNA formatted sequences::
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64
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65 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
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66 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg
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67 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag
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68 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc
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69 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc
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70 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg
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71
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72 Running this tool will produce this::
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73
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74 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other;
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75 orf00001 577 699 +1 5.24
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76 orf00003 800 1123 +2 5.18
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77 orf00004 1144 3813 +1 10.62
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78 orf00006 3857 6220 +2 6.07
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79 orf00007 6226 7173 +1 1.69
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80 orf00008 7187 9307 +2 8.95
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81 orf00009 9424 10410 +1 8.29
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82 orf00010 10515 11363 +3 7.00
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83 orf00011 11812 11964 +1 2.80
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84 orf00012 12360 13457 +3 4.80
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85 orf00013 14379 14044 -1 7.41
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86 orf00015 15029 14739 -3 12.43
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87 orf00016 15066 15227 +3 1.91
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88 orf00020 16061 15351 -3 2.83
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89 orf00021 17513 17391 -3 2.20
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90 orf00023 17529 17675 +3 0.11
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91
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92
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93 -------
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94
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95 **References**
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96
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97 A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007).
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98
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99 </help>
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100 </tool>
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