Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/anosim.xml @ 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 04 Dec 2012 11:05:19 -0600 |
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1 <tool id="mothur_anosim" name="Anosim" version="1.19.0"> |
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2 <description>Non-parametric multivariate analysis of changes in community structure</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='anosim' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.anosim$:'$anosim |
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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=$alpha |
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15 #end if |
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16 </command> |
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17 <inputs> |
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18 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
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19 <param name="design" type="data" format="tabular" label="design - assign groups to new grouping" |
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20 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/> |
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21 <param name="alpha" type="float" optional="true" value="0.05" label="alpha - acceptable stopping precision (default 0.05)"/> |
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22 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> |
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23 </inputs> |
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24 <outputs> |
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25 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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26 <data format="tabular" name="anosim" label="${tool.name} on ${on_string}: anosim"/> |
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27 </outputs> |
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28 <requirements> |
27
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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 anosim_ command uses a phylip_distance_matrix_ and a design file to calculate the non-parametric multivariate analysis of changes in community structure. |
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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 .. _anosim: http://www.mothur.org/wiki/Anosim |
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60 |
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61 |
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62 </help> |
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63 </tool> |