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1 <tool id="GeCoS" name="GeCoS" version="1.0.0">
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2 <description>(GeneCodonSearch) calculates the codon composition in a DNA sequence.</description>
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3 <command interpreter="python">GeneCodonSearch1_2.py -c $codon -m $minimum -i $input_sequences -r $resultfile</command>
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4 <inputs>
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5 <param type="data" format="fasta" name="input_sequences" label="Input Sequences"/>
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6 <param name="codon" type="select" label="Codons" multiple="true">
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7 <option value="ATA" selected="false">ATG</option>
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8 <option value="ATC" selected="false">ATC</option>
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9 <option value="ATT" selected="false">ATT</option>
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10 <option value="ATG" selected="false">ATG</option>
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11 <option value="ACA" selected="false">ACA</option>
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12 <option value="ACC" selected="false">ACC</option>
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13 <option value="ACG" selected="false">ACG</option>
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14 <option value="ACT" selected="false">ACT</option>
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15 <option value="AAC" selected="false">AAC</option>
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16 <option value="AAT" selected="false">AAT</option>
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17 <option value="AAA" selected="false">AAA</option>
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18 <option value="AAG" selected="false">AAG</option>
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19 <option value="AGC" selected="false">AGC</option>
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20 <option value="AGT" selected="false">AGT</option>
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21 <option value="AGA" selected="false">AGA</option>
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22 <option value="AGG" selected="false">AGG</option>
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23 <option value="CTA" selected="false">CTA</option>
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24 <option value="CTC" selected="false">CTC</option>
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25 <option value="CTG" selected="false">CTG</option>
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26 <option value="CTT" selected="false">CTT</option>
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27 <option value="CCA" selected="false">CCA</option>
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28 <option value="CCC" selected="false">CCC</option>
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29 <option value="CCG" selected="false">CCG</option>
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30 <option value="CCT" selected="false">CCT</option>
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31 <option value="CAC" selected="false">CAC</option>
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32 <option value="CAT" selected="false">CAT</option>
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33 <option value="CAA" selected="false">CAA</option>
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34 <option value="CAG" selected="false">CAG</option>
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35 <option value="CGA" selected="false">CGA</option>
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36 <option value="CGC" selected="false">CGC</option>
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37 <option value="CGG" selected="false">CGG</option>
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38 <option value="CGT" selected="false">CGT</option>
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39 <option value="GTA" selected="false">GTA</option>
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40 <option value="GTC" selected="false">GTC</option>
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41 <option value="GTG" selected="false">GTG</option>
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42 <option value="GTT" selected="false">GTT</option>
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43 <option value="GCA" selected="false">GCA</option>
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44 <option value="GCC" selected="false">GCC</option>
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45 <option value="GCG" selected="false">GCG</option>
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46 <option value="GCT" selected="false">GCT</option>
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47 <option value="GAC" selected="false">GAC</option>
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48 <option value="GAT" selected="false">GAT</option>
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49 <option value="GAA" selected="false">GAA</option>
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50 <option value="GAG" selected="false">GAG</option>
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51 <option value="GGA" selected="false">GGA</option>
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52 <option value="GGC" selected="false">GGC</option>
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53 <option value="GGG" selected="false">GGG</option>
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54 <option value="GGT" selected="false">GGT</option>
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55 <option value="TCA" selected="false">TCA</option>
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56 <option value="TCC" selected="false">TCC</option>
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57 <option value="TCG" selected="false">TCG</option>
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58 <option value="TCT" selected="false">TCT</option>
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59 <option value="TTC" selected="false">TTC</option>
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60 <option value="TTT" selected="false">TTT</option>
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61 <option value="TTA" selected="false">TTA</option>
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62 <option value="TTG" selected="false">TTG</option>
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63 <option value="TAC" selected="false">TAC</option>
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64 <option value="TAT" selected="false">TAT</option>
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65 <option value="TAA" selected="false">TAA</option>
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66 <option value="TAG" selected="false">TAG</option>
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67 <option value="TGC" selected="false">TGC</option>
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68 <option value="TGT" selected="false">TGT</option>
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69 <option value="TGA" selected="false">TGA</option>
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70 <option value="TGG" selected="false">TGG</option>
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71 </param>
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72 <param name="minimum" type="float" value="0.0" label="Minimum codon content (cutoff)"/>
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73 </inputs>
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74 <outputs>
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75 <data format="txt" name="resultfile"/>
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76 </outputs>
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77
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78 <help>
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79 **What it does**
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80 **GeCos** is a tool that calculates the codon composition of any given DNA sequence.
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81
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82 **Input**
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83
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84 - If more than one sequence is analyzed at a time, a **cutoff value** can be used to filter the output. Only the sequences with a higher total score than the cutoff value will be displayed in the output.
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85
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86 - The DNA sequence(s), that are supposed to be analyzed with GeCoS need to be formatted as fasta.
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87
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88 Example::
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89
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90 >CCE57618 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:166:1143:1 gene:HUS2011_pII0001 description:replication initiation protein RepFIB
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91 GTGGATAAGTC ... TCTTCAAATCCCGCTGA
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92 >CCE57620 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:1422:2162:-1 gene:HUS2011_pII0003 description:site-specific recombinase
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93 ATGAACAATG ... CTCCCCTGAAGTAA
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94 >CCE57621 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:2531:2692:-1 gene:HUS2011_pII0004 description:plasmid stabilisation system family protein
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95 ATGAGTAATCA ... ATTTCAACTGA
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96 >CCE57622 cdna plasmid:HUSEC2011CHR1:pHUSEC2011-2:2894:3076:-1 gene:HUS2011_pII0005 description:putative transcriptional regulator
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97 ATGGCCAG ... AGAAGGCT
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98
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99 **Output**
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100
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101 - GeCoS produces a matrix containing the identifier used in the input, the combined score of the sequence and the number of each of the chosen codons.
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102
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103 - **Total Score** = sum of codon occurences / sequence length * number of analyzed codons
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104
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105 - The output is sorted from low to high (Total Score: 0 to 1).
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106
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107 Example::
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108
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109 [['Gene_ID' 'Total Score' 'AGG' 'AGC' 'CCC' 'TGC' 'GCG']
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110 ['CCE57562' 0.0190476 1 3 1 2 1]
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111 ['CCQ29559' 0.0190476 0 1 2 2 1]
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112 ...
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113 ['CCQ31238' 0.0328358 0 3 0 6 2]
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114 ['CCE57539' 0.05 2 0 4 3 3]]
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115
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116 </help>
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117
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118 </tool>
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