Mercurial > repos > dazeone > kaks_calculator
changeset 3:38170fd7e7ea draft
Deleted selected files
| author | dazeone |
|---|---|
| date | Thu, 18 Mar 2021 14:38:31 +0000 |
| parents | e0eca61ba34b |
| children | 7e5ed927562f |
| files | kaks.xml |
| diffstat | 1 files changed, 0 insertions(+), 84 deletions(-) [+] |
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--- a/kaks.xml Thu Mar 18 14:33:38 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ -<tool id="kakstool" name="kaks_calculator" version="2.0.1"> -<description> A toolbox based on integrating gamma methods and sliding window strategy </description> - - <requirements> - <requirement type="package" version="2.0.1">kakscalculator2</requirement> -</requirements> - -<command>KaKs_Calculator '-i' $input '-c' $c '-m' $m '-o' $output </command> - -<inputs> - <param format="axt" name="input" type="data" label="Axt alignment files :" multiple="true" display="checkboxes"/> - -<param name="c" type="select" label="Genetic code table (Default = 1-Standard Code):"> -<option value="1">Standard Code</option> -<option value="2">Vertebrate Mitochondrial Code</option> -<option value="3">Yeast Mitochondrial Code</option> -<option value="4">Mold Mitochondrial Code</option> -<option value="5">Invertebrate Mitochondrial Code</option> -<option value="6">Ciliate, Dasycladacean and Hexamita Code</option> - -<option value="10">Euplotid Nuclear Code</option> -<option value="11">Bacterial and Plant Plastid Code</option> -<option value="12">Alternative Yeast Nuclear Code</option> -<option value="13">Ascidian Mitochondrial Code</option> -<option value="14">Alternative Flatworm Mitochondrial Code</option> -<option value="15">Blepharisma Nuclear Code</option> -<option value="16">Chlorophycean Mitochondrial Code</option> - -<option value="21">Trematode Mitochondrial Code</option> -<option value="22">Scenedesmus obliquus mitochondrial Code</option> -<option value="23">Thraustochytrium Mitochondrial Code</option> -</param> - - - -<param name="m" type="select" label="Methods for estimating Ka and Ks and theirs references (Default = MA) :"> -<option value="NG">NG (Nei, M. and Gojobori, T. (1986) Mol. Biol. Evol., 3, 418-426.)</option> -<option value="LWL">LWL (Li, W.H., Wu, C.I. and Luo, C.C. (1985) Mol. Biol. Evol., 2, 150-174.)</option> -<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> -<option value="MLWL">MLWL (Tzeng, Y.H., Pan, R. and Li, W.H. (2004) Mol. Biol. Evol., 21, 2290-2298.)</option> -<option value="MLPB">MLPB (Tzeng, Y.H., Pan, R. and Li, W.H. (2004) Mol. Biol. Evol., 21, 2290-2298.)</option> -<option value="GY">GY (Goldman, N. and Yang, Z. (1994) Mol. Biol. Evol., 11, 725-736.)</option> -<option value="YN">YN (Yang, Z. and Nielsen, R. (2000) Mol. Biol. Evol., 17, 32-43.)</option> -<option value="MYN">MYN (Zhang, Z., Li, J. and Yu, J. (2006) BMC Evolutionary Biology, 6, 44.)</option> -<option value="MS">MS (Model Selection according to the AICc)</option> -<option value="MA">MA ( Model Averaging on a set of candidate models) </option> -<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> -<option value="GLWL">GLWL (same)</option> -<option value="GLPB">GLPB (same)</option> -<option value="GMLWL">GMLWL (same)</option> -<option value="GYN">GYN (same)</option> -<option value="GMYN">GMYN (Wang, DP., Wan, HL., Zhang, S. and Yu, J. (2009) Biology Direct, 4:20 (16 June 2009)) </option> -</param> - -</inputs> - -<outputs> -<data format="tabular" name="output"/> -</outputs> - -<tests> - <test> - <param name="input" value="example.axt" /> - <param name="c" value="1"/> -<param name="m" value="NG"/> - <output name="output" file="out" /> - </test> -</tests> - -<help> --Please send bugs or advice to Da-Peng Wang at wangdp@big.ac.cn or Yu-Bin Zhang at ybzhang@big.ac.cn. - --More information about the Genetic Codes: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c - </help> - -<citations> -<citation type="doi">10.1016/S1672-0229(10)60008-3</citation> - - <citation type="doi">10.1186/1745-6150-4-20</citation> - - <citation type="doi">S1672-0229(08)60040-6</citation> - -</citations> -</tool>