Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/amova.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
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children | 95d75b35e4d2 |
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1 <tool id="mothur_amova" name="Amova" version="1.19.0"> |
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2 <description>Analysis of molecular variance</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='amova' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.amova$:'$amova |
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7 --outputdir='$logfile.extra_files_path' |
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8 --phylip=$dist |
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9 --design=$design |
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10 #if int($iters.__str__) > 0: |
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11 --iters=$iters |
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12 #end if |
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13 #if float($alpha.__str__) > 0.0: |
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14 --alpha=$alpha |
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15 #end if |
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16 </command> |
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17 <inputs> |
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18 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
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19 <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" |
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20 help="design has 2 TAB-separated columns: group and grouping (Tool: Make_Design) "/> |
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21 <param name="alpha" type="float" optional="true" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/> |
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22 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> |
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23 </inputs> |
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24 <outputs> |
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25 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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26 <data format="tabular" name="amova" label="${tool.name} on ${on_string}: amova"/> |
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27 </outputs> |
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28 <requirements> |
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29 <requirement type="package" version="1.27">mothur</requirement> |
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30 </requirements> |
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31 <tests> |
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32 </tests> |
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33 <help> |
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34 **Mothur Overview** |
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35 |
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36 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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37 in the Department of Microbiology and Immunology at The University of Michigan, |
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38 provides bioinformatics for the microbial ecology community. |
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39 |
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40 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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41 |
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42 **Command Documenation** |
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43 |
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44 The amova_ command calculates the analysis of molecular variance from a phylip_distance_matrix_, a nonparametric analog of traditional analysis of variance. This method is widely used in population genetics to test the hypothesis that genetic diversity within two populations is not significantly different from that which would result from pooling the two populations. |
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45 |
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46 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. : |
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47 ======= ======= |
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48 duck bird |
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49 cow mammal |
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50 pig mammal |
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51 goose bird |
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52 cobra reptile |
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53 ======= ======= |
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54 |
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55 The Make_Design tool can construct a design file from a Mothur dataset that contains group names. |
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56 |
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57 |
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58 .. _phylip_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix |
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59 .. _amova: http://www.mothur.org/wiki/Amova |
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60 |
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61 |
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62 </help> |
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63 </tool> |