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1 <tool id="glimmer_build-icm" name="Glimmer ICM builder" version="0.2">
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2 <description></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 </requirements>
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6 <command>
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7 build-icm
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8 --depth $depth
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9 #if $no_stops:
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10 --no_stops
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11 #end if
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12 --period $period
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13 --width $width
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14
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15 #if $stop_codon_opts.stop_codon_opts_selector == "gb":
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16 --trans_table "${stop_codon_opts.genbank_gencode}"
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17 #else:
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18 --stop_codons "${stop_codon_opts.stop_codons}"
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19 #end if
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20
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21 $outfile < $infile 2>&1;
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22 </command>
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23 <inputs>
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24 <param name="infile" type="data" format="fasta" label="Trainings Dataset" help="A set of known genes in FASTA format." />
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25 <param name="depth" type="integer" value="7" label="Set the depth of the ICM" help="The depth is the maximum number of positions in the context window that will be used to determine the probability of the predicted position." />
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26 <param name="period" type="integer" value="3" label="Set the period of the ICM" help="The period is the number of different submodels for different positions in the text in a cyclic pattern. E.g., if the period is 3, the first submodel will determine positions 1, 4, 7, ..." />
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27 <param name="width" type="integer" value="12" label="Set the width of the ICM" help="The width includes the predicted position." />
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28 <param name="no_stops" type="boolean" truevalue="--no_stops" falsevalue="" checked="false" label="Do not use any input strings with in-frame stop codons" />
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29
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30 <conditional name="stop_codon_opts">
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31 <param name="stop_codon_opts_selector" type="select" label="Specify start codons as">
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32 <option value="gb" selected="True">Genbank translation table entry</option>
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33 <option value="free_form">Comma-separated list</option>
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34 </param>
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35 <when value="gb">
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36 <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons">
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37 <option value="1" select="True">1. Standard</option>
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38 <option value="2">2. Vertebrate Mitochondrial</option>
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39 <option value="3">3. Yeast Mitochondrial</option>
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40 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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41 <option value="5">5. Invertebrate Mitochondrial</option>
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42 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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43 <option value="9">9. Echinoderm Mitochondrial</option>
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44 <option value="10">10. Euplotid Nuclear</option>
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45 <option value="11">11. Bacteria and Archaea</option>
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46 <option value="12">12. Alternative Yeast Nuclear</option>
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47 <option value="13">13. Ascidian Mitochondrial</option>
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48 <option value="14">14. Flatworm Mitochondrial</option>
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49 <option value="15">15. Blepharisma Macronuclear</option>
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50 <option value="16">16. Chlorophycean Mitochondrial</option>
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51 <option value="21">21. Trematode Mitochondrial</option>
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52 <option value="22">22. Scenedesmus obliquus mitochondrial</option>
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53 <option value="23">23. Thraustochytrium Mitochondrial</option>
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54 <option value="24">24. Pterobranchia mitochondrial</option>
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55 </param>
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56 </when>
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57 <when value="free_form">
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58 <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" />
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59 </when>
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60 </conditional>
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61 </inputs>
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62 <outputs>
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63 <data format="data" name="outfile" />
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="infile" value='streptomyces_Tu6071_plasmid_genes.fasta' />
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68 <param name="depth" value="7" />
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69 <param name="period" value="3" />
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70 <param name="width" value="12" />
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71 <param name="no_stops" value="" />
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72 <param name="genbank_gencode" value="11" />
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73 <!-- compare files sizes, because the output is a binary -->
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74 <output name="outfile" file='streptomyces_Tu6071_plasmid_genes.icm' compare="sim_size" delta="1000" ftype="data" />
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75 </test>
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76 </tests>
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77
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78 <help>
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79
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80 **What it does**
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81
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82 This program constructs an interpolated context model (ICM) from an input set of sequences.
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83
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84 This model can be used by Glimmer3 to predict genes.
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85
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86 **TIP** To extract CDS from a GenBank file use the tool *Extract ORF from a GenBank file*.
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87
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88 -----
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89
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90 **Example**
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91
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92 *Input*::
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93
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94 - Genome Sequence
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95
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96 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
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97 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
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98 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
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99 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
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100 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
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101 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
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102 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
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103 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
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104 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
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105 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
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106 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
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107 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
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108 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
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109 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
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110 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
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111 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
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112 .....
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113
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114 *Output*::
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115 interpolated context model (ICM)
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116
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117 -------
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118
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119 **References**
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120
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121 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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122
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123
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124 </help>
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125 </tool>
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