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1 <tool id="glimmer_knowlegde-based" name="Glimmer3" version="0.2">
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2 <description>Predict ORFs in prokaryotic genomes (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 <requirement type="set_environment">GLIMMER_SCRIPT_PATH</requirement>
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7 </requirements>
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8 <command>
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9 #import tempfile, os
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10 #set $temp = tempfile.NamedTemporaryFile( delete=False )
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11 #silent $temp.close()
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12 #set $temp = $temp.name
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13
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14 glimmer3
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15 --max_olap $max_olap
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16 --gene_len $gene_len
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17 --threshold $threshold
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18 #if float( str($gc_percent) ) > 0.0:
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19 --gc_percent $gc_percent
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20 #end if
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21
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22 #if $stop_codon_opts.stop_codon_opts_selector == "gb":
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23 --trans_table "${stop_codon_opts.genbank_gencode}"
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24 #else:
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25 --stop_codons "${stop_codon_opts.stop_codons}"
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26 #end if
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27
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28 --start_codons $start_codons
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29
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30 $linear
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31 $no_indep
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32 $extend
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33 $seq_input
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34 $icm_input
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35 $temp 2>&1;
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36
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37 ## convert prediction to FASTA sequences
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38 \$GLIMMER_SCRIPT_PATH/glimmer2seq.py $temp".predict" $seq_input $genes_output;
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39
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40 #if $report:
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41 mv $temp".predict" $report_output;
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42 #else:
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43 rm $temp".predict";
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44 #end if
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45
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46 #if $detailed_report:
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47 mv $temp".detail" $detailed_output;
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48 #else:
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49 rm $temp".detail";
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50 #end if
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51
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52 rm $temp
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53 </command>
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54 <inputs>
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55 <param name="seq_input" type="data" format="fasta" label="Genome Sequence" />
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56 <param name="icm_input" type="data" format="data" label="Interpolated context model (ICM)" />
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57
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58 <param name="max_olap" type="integer" value="50" label="Set maximum overlap length" help="Overlaps this short or shorter are ignored." />
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59 <param name="gene_len" type="integer" value="90" label="Set the minimum gene length to n nucleotides" hrlp="This does not include the bases in the stop codon."/>
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60 <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene" help="If the in-frame score >= N, then the region is given a number and considered a potential gene." />
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61 <param name="gc_percent" type="float" value="0.0" label="Set the GC percentage of the independent model, i.e., the model of intergenic sequence" help="If 0.0 specified, the GC percentage will be counted from the input file." />
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62
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63 <param name="linear" type="boolean" truevalue="--linear" falsevalue="" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" />
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64 <param name="no_indep" type="boolean" truevalue="--no_indep" falsevalue="" checked="false" label="Don’t use the independent probability score column at all" help="Using this option will produce more short gene predictions." />
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65 <param name="extend" type="boolean" truevalue="--extend" falsevalue="" checked="false" label="Also score orfs that extend off the end of the sequence(s)" />
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66 <param name="start_codons" type="text" value="atg,gtg,ttg" label="Specify start codons as a comma-separated list" />
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67
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68 <conditional name="stop_codon_opts">
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69 <param name="stop_codon_opts_selector" type="select" label="Specify start codons as">
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70 <option value="gb" selected="True">Genbank translation table entry</option>
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71 <option value="free_form">Comma-separated list</option>
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72 </param>
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73 <when value="gb">
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74 <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons">
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75 <option value="1" select="True">1. Standard</option>
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76 <option value="2">2. Vertebrate Mitochondrial</option>
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77 <option value="3">3. Yeast Mitochondrial</option>
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78 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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79 <option value="5">5. Invertebrate Mitochondrial</option>
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80 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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81 <option value="9">9. Echinoderm Mitochondrial</option>
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82 <option value="10">10. Euplotid Nuclear</option>
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83 <option value="11">11. Bacteria and Archaea</option>
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84 <option value="12">12. Alternative Yeast Nuclear</option>
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85 <option value="13">13. Ascidian Mitochondrial</option>
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86 <option value="14">14. Flatworm Mitochondrial</option>
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87 <option value="15">15. Blepharisma Macronuclear</option>
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88 <option value="16">16. Chlorophycean Mitochondrial</option>
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89 <option value="21">21. Trematode Mitochondrial</option>
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90 <option value="22">22. Scenedesmus obliquus mitochondrial</option>
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91 <option value="23">23. Thraustochytrium Mitochondrial</option>
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92 <option value="24">24. Pterobranchia mitochondrial</option>
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93 </param>
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94 </when>
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95 <when value="free_form">
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96 <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" />
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97 </when>
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98 </conditional>
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99
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100 <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output"/>
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101 <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file"/>
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102 </inputs>
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103 <outputs>
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104 <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" />
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105 <data name="report_output" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)">
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106 <filter>report == True</filter>
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107 </data>
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108 <data name="detailed_output" format="txt" label="Glimmer3 on ${on_string} (detailed report)">
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109 <filter>detailed_report == True</filter>
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110 </data>
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111 </outputs>
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112 <tests>
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113 <test>
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114 <param name="seq_input" value='streptomyces_Tu6071_genomic.fasta' />
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115 <param name="icm_input" value='streptomyces_Tu6071_plasmid_genes.icm' />
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116 <param name="max_olap" value="50" />
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117 <param name="gene_len" value="90" />
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118 <param name="threshold" value="30" />
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119 <param name="gc_percent" value="0.0" />
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120 <param name="linear" value="--linear" />
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121 <param name="no_indep" value="" />
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122 <param name="extend" value="" />
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123 <param name="start_codons" value="atg,gtg,ttg" />
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124 <param name="genbank_gencode" value="11" />
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125 <param name="detailed_report" value="" />
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126 <param name="report" value="" />
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127 <output name="genes_output" file='glimmer_w_icm_trans-table-11_genomic.fasta' ftype="fasta" />
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128 </test>
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129 </tests>
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130 <help>
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131
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132
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133 **What it does**
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134
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135 This is the main program that makes gene preditions based on an interpolated context model (ICM).
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136
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137 The ICM can be generated with extracted CDS from related organisms (ICM builder). If you can't generate an ICM model you can use the non knowlegde-based Glimmer with a de novo prediction.
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138
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139 -----
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140
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141 **Example**
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142
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143 *Input*::
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144
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145 - interpolated context model (ICM): Use the 'Glimmer ICM builder' tool to create one
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146 - Genome Sequence in FASTA format
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147
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148 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7
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149 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT
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150 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT
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151 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT
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152 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC
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153 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA
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154 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG
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155 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA
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156 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA
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157 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC
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158 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA
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159 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC
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160 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC
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161 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA
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162 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC
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163 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT
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164 .....
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165
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166 *Output*::
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167
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168 - FASTA file with predicted proteins
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169 - Glimmer prediction file (optional)
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170
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171 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7.
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172 orf00001 40137 52 +2 8.68
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173 orf00004 603 34 -1 2.91
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174 orf00006 1289 1095 -3 3.16
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175 orf00007 1555 1391 -2 2.33
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176 orf00008 1809 1576 -1 1.02
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177 orf00010 1953 2066 +3 3.09
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178 orf00011 2182 2304 +1 0.89
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179 orf00013 2390 2521 +2 0.60
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180 orf00018 2570 3073 +2 2.54
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181 orf00020 3196 3747 +1 2.91
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182 orf00022 3758 4000 +2 0.83
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183 orf00023 4399 4157 -2 1.31
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184 orf00025 4463 4759 +2 2.92
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185 orf00026 4878 5111 +3 0.78
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186 orf00027 5468 5166 -3 1.64
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187 orf00029 5590 5832 +1 0.29
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188 orf00032 6023 6226 +2 6.02
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189 orf00033 6217 6336 +1 3.09
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190 ........
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191
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192 - Glimmer detailed report (optional)
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193
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194 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7.
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195 Sequence length = 40222
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196
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197 ----- Start ----- --- Length ---- ------------- Scores -------------
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198 ID Frame of Orf of Gene Stop of Orf of Gene Raw InFrm F1 F2 F3 R1 R2 R3 NC
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199 0001 +2 40137 40137 52 135 135 9.26 96 - 96 - - 3 - 0
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200 0002 +1 58 64 180 120 114 5.01 69 69 - - 30 - - 0
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201 +3 300 309 422 120 111 -0.68 20 - - 20 38 - - 41
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202 +3 423 432 545 120 111 1.29 21 - 51 21 13 - 8 5
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203 0003 +2 401 416 595 192 177 2.51 93 - 93 - 5 - - 1
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204 0004 -1 645 552 34 609 516 2.33 99 - - - 99 - - 0
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205 +1 562 592 762 198 168 -2.54 1 1 - - - - - 98
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206 +1 763 772 915 150 141 -1.34 1 1 - - - - 86 11
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207 +3 837 846 1007 168 159 1.35 28 - 50 28 - - 17 3
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208 0005 -3 1073 977 654 417 321 0.52 84 - - - - - 84 15
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209 0006 -3 1373 1319 1095 276 222 3.80 99 - - - - - 99 0
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210 0007 -2 1585 1555 1391 192 162 2.70 98 - - - - 98 - 1
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211 0008 -1 1812 1809 1576 234 231 1.26 94 - - - 94 - - 5
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212 0009 +2 1721 1730 1945 222 213 0.68 80 - 80 - - - - 19
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213 .....
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214
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215 -------
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216
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217 **References**
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218
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219 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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220
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221
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222 </help>
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223
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224 </tool>
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