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1 <tool id="kakstool" name="kaks_calculator" version="2.0.1">
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2 <description> A toolbox based on integrating gamma methods and sliding window strategy </description>
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3
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4 <requirements>
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5 <requirement type="package" version="2.0.1">kakscalculator2</requirement>
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6 </requirements>
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7
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8 <command>KaKs_Calculator '-i' $input '-c' $c '-m' $m '-o' $output </command>
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9
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10 <inputs>
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11 <param format="axt" name="input" type="data" label="Axt alignment files :" multiple="true" display="checkboxes"/>
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12
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13 <param name="c" type="select" label="Genetic code table (Default = 1-Standard Code):">
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14 <option value="1">Standard Code</option>
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15 <option value="2">Vertebrate Mitochondrial Code</option>
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16 <option value="3">Yeast Mitochondrial Code</option>
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17 <option value="4">Mold Mitochondrial Code</option>
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18 <option value="5">Invertebrate Mitochondrial Code</option>
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19 <option value="6">Ciliate, Dasycladacean and Hexamita Code</option>
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20
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21 <option value="10">Euplotid Nuclear Code</option>
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22 <option value="11">Bacterial and Plant Plastid Code</option>
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23 <option value="12">Alternative Yeast Nuclear Code</option>
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24 <option value="13">Ascidian Mitochondrial Code</option>
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25 <option value="14">Alternative Flatworm Mitochondrial Code</option>
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26 <option value="15">Blepharisma Nuclear Code</option>
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27 <option value="16">Chlorophycean Mitochondrial Code</option>
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28
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29 <option value="21">Trematode Mitochondrial Code</option>
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30 <option value="22">Scenedesmus obliquus mitochondrial Code</option>
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31 <option value="23">Thraustochytrium Mitochondrial Code</option>
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32 </param>
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33
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34
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35
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36 <param name="m" type="select" label="Methods for estimating Ka and Ks and theirs references (Default = MA) :">
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37 <option value="NG">NG (Nei, M. and Gojobori, T. (1986) Mol. Biol. Evol., 3, 418-426.)</option>
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38 <option value="LWL">LWL (Li, W.H., Wu, C.I. and Luo, C.C. (1985) Mol. Biol. Evol., 2, 150-174.)</option>
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39 <option value="LPB">LPB (Li, W.H. (1993) J. Mol. Evol., 36, 96-99. Pamilo, P. and Bianchi, N.O. (1993) Mol. Biol. Evol., 10, 271-281.</option>
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40 <option value="MLWL">MLWL (Tzeng, Y.H., Pan, R. and Li, W.H. (2004) Mol. Biol. Evol., 21, 2290-2298.)</option>
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41 <option value="MLPB">MLPB (Tzeng, Y.H., Pan, R. and Li, W.H. (2004) Mol. Biol. Evol., 21, 2290-2298.)</option>
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42 <option value="GY">GY (Goldman, N. and Yang, Z. (1994) Mol. Biol. Evol., 11, 725-736.)</option>
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43 <option value="YN">YN (Yang, Z. and Nielsen, R. (2000) Mol. Biol. Evol., 17, 32-43.)</option>
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44 <option value="MYN">MYN (Zhang, Z., Li, J. and Yu, J. (2006) BMC Evolutionary Biology, 6, 44.)</option>
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45 <option value="MS">MS (Model Selection according to the AICc)</option>
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46 <option value="MA">MA ( Model Averaging on a set of candidate models) </option>
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47 <option value="GNG">GNG (Wang, DP., Zhang, S., He, FH., Zhu, J.,Hu, SN. and Yu, J.(2009) Genomics, Proteomics and Bioinformatics. In press.) </option>
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48 <option value="GLWL">GLWL (same)</option>
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49 <option value="GLPB">GLPB (same)</option>
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50 <option value="GMLWL">GMLWL (same)</option>
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51 <option value="GYN">GYN (same)</option>
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52 <option value="GMYN">GMYN (Wang, DP., Wan, HL., Zhang, S. and Yu, J. (2009) Biology Direct, 4:20 (16 June 2009)) </option>
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53 </param>
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54
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55 </inputs>
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56
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57 <outputs>
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58 <data format="tabular" name="output"/>
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59 </outputs>
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60
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61 <tests>
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62 <test>
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63 <param name="input" value="example.axt" />
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64 <param name="c" value="1"/>
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65 <param name="m" value="NG"/>
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66 <output name="output" file="out" />
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67 </test>
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68 </tests>
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69
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70 <help>
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71 -Please send bugs or advice to Da-Peng Wang at wangdp@big.ac.cn or Yu-Bin Zhang at ybzhang@big.ac.cn.
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72
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73 -More information about the Genetic Codes: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
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74 </help>
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75
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76 <citations>
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77 <citation type="doi">10.1016/S1672-0229(10)60008-3</citation>
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78
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79 <citation type="doi">10.1186/1745-6150-4-20</citation>
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80
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81 <citation type="doi">S1672-0229(08)60040-6</citation>
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82
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83 </citations>
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84 </tool>
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