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1 <?xml version="1.0"?>
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2 <tool name="Codon Switch Tool" id="codon_switch" version="0.2.6">
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3 <description>for each sequence in a file</description>
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4 <requirements>
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5 <requirement type="package" version="2.7.15">python</requirement>
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6 <requirement type="package" version="1.72">biopython</requirement>
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7 <requirement type="package" version="0.23.4">pandas</requirement>
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8 <requirement type="package" version="1.15.3">numpy</requirement>
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9 </requirements>
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10
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11 <command>
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12 <![CDATA[
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13 python '$__tool_directory__/codon_switch.py' -i $input -l $input_type -p $patterns -g $genome -g $genome_type -c $codon_table -f $num_plasmids -m $row_len -d $demonstration -o $output
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="input" format="genbank" type="data" label="Input plasmid"/>
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18
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19 <param name="input_type" type="select" format="text">
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20 <label>Indicate the input file format.</label>
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21 <option value="genbank">genbank</option>
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22 </param>
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23
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24 <param name="patterns" format="txt" type="data" label="Patterns file"/>
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25
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26 <param name="genome" format="genbank" type="data" label="Input Genome"/>
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27
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28 <param name="genome_type" type="select" format="text">
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29 <label>Indicate the input genome format.</label>
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30 <option value="fasta">fasta</option>
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31 <option value="genbank">genbank</option>
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32 </param>
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33
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34 <param name="demonstration" type="select" format="text">
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35 <label>Demonstration</label>
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36 <option value="demonstration">yes</option>
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37 <option value="no_demonstration">no</option>
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38 </param>
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39
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40 <param name="num_plasmids" type="select" format="text">
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41 <label>Indicate the number of best output plamids.</label>
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42 <option value=3>3</option>
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43 <option value=7>7</option>
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44 </param>
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45
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46 <param name="row_len" type="select" format="text">
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47 <label>Indicate the length of the row in report file.</label>
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48 <option value=9>9</option>
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49 <option value=27>27</option>
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50 </param>
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51
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52 <param name="codon_table" type="select" format="text">
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53 <label>Choose the proper codon table for your organism.</label>
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54 <option value="Alternative Flatworm Mitochondrial">"Alternative Flatworm Mitochondrial"</option>
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55 <option value="Alternative Yeast Nuclear">"Alternative Yeast Nuclear"</option>
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56 <option value="Archaeal">"Archaeal"</option>
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57 <option value="Ascidian Mitochondrial">"Ascidian Mitochondrial"</option>
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58 <option value="Bacterial">"Bacterial"</option>
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59 <option value="Blastocrithidia Nuclear">"Blastocrithidia Nuclear"</option>
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60 <option value="Blepharisma Macronuclear">"Blepharisma Macronuclear"</option>
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61 <option value="Candidate Division SR1">"Candidate Division SR1"</option>
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62 <option value="Chlorophycean Mitochondrial">"Chlorophycean Mitochondrial"</option>
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63 <option value="Ciliate Nuclear">"Ciliate Nuclear"</option>
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64 <option value="Coelenterate Mitochondrial">"Coelenterate Mitochondrial"</option>
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65 <option value="Condylostoma Nuclear">"Condylostoma Nuclear"</option>
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66 <option value="Dasycladacean Nuclear">"Dasycladacean Nuclear"</option>
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67 <option value="Echinoderm Mitochondrial">"Echinoderm Mitochondrial"</option>
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68 <option value="Euplotid Nuclear">"Euplotid Nuclear"</option>
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69 <option value="Flatworm Mitochondrial">"Flatworm Mitochondrial"</option>
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70 <option value="Gracilibacteria">"Gracilibacteria"</option>
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71 <option value="Hexamita Nuclear">"Hexamita Nuclear"</option>
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72 <option value="Invertebrate Mitochondrial">"Invertebrate Mitochondrial"</option>
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73 <option value="Karyorelict Nuclear">"Karyorelict Nuclear"</option>
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74 <option value="Mesodinium Nuclear">"Mesodinium Nuclear"</option>
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75 <option value="Mold Mitochondrial">"Mold Mitochondrial"</option>
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76 <option value="Mycoplasma">"Mycoplasma"</option>
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77 <option value="Pachysolen tannophilus Nuclear">"Pachysolen tannophilus Nuclear"</option>
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78 <option value="Peritrich Nuclear">"Peritrich Nuclear"</option>
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79 <option value="Plant Plastid">"Plant Plastid"</option>
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80 <option value="Protozoan Mitochondrial">"Protozoan Mitochondrial"</option>
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81 <option value="Pterobranchia Mitochondrial">"Pterobranchia Mitochondrial"</option>
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82 <option value="SGC0">"SGC0"</option>
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83 <option value="SGC1">"SGC1"</option>
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84 <option value="SGC2">"SGC2"</option>
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85 <option value="SGC3">"SGC3"</option>
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86 <option value="SGC4">"SGC4"</option>
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87 <option value="SGC5">"SGC5"</option>
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88 <option value="SGC8">"SGC8"</option>
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89 <option value="SGC9">"SGC9"</option>
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90 <option value="Scenedesmus obliquus Mitochondrial">"Scenedesmus obliquus Mitochondrial"</option>
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91 <option value="Spiroplasma">"Spiroplasma"</option>
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92 <option value="Standard">"Standard"</option>
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93 <option value="Thraustochytrium Mitochondrial">"Thraustochytrium Mitochondrial"</option>
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94 <option value="Trematode Mitochondrial">"Trematode Mitochondrial"</option>
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95 <option value="Vertebrate Mitochondrial">"Vertebrate Mitochondrial"</option>
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96 <option value="Yeast Mitochondrial">"Yeast Mitochondrial"</option>
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97 </param>
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98 </inputs>
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99
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100 <outputs>
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101 <data format="tabular" name="output" />
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102 </outputs>
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103
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104 <help>
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105 This tool permits codon switch and transversion in targeted regions.
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106 </help>
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107 </tool>
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