Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/mantel.xml @ 15:a6189f58fedb
Mothur - updated for Mothur version 1.22.0
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 08 Nov 2011 11:45:32 -0600 |
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1 <tool id="mothur_mantel" name="Mantel" version="1.19.0"> |
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2 <description>Mantel correlation coefficient between two matrices.</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='mantel' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.mantel$:'$mantel |
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7 --outputdir='$logfile.extra_files_path' |
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8 --phylip=$dist |
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9 --phylip2=$dist2 |
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10 --method=$method |
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11 #if int($iters.__str__) > 0: |
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12 --iters=$iters |
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13 #end if |
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14 </command> |
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15 <inputs> |
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16 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> |
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17 <param name="dist2" type="data" format="lower.dist,square.dist" label="phylip2 - Distance Matrix"/> |
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18 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson" > |
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19 <option value="pearson" selected="true">pearson</option> |
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20 <option value="spearman">spearman</option> |
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21 <option value="kendall">kendall</option> |
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22 </param> |
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23 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/> |
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24 </inputs> |
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25 <outputs> |
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26 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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27 <data format="tabular" name="mantel" label="${tool.name} on ${on_string}: mantel"/> |
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28 </outputs> |
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29 <requirements> |
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30 <requirement type="binary">mothur</requirement> |
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31 </requirements> |
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32 <tests> |
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33 </tests> |
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34 <help> |
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35 **Mothur Overview** |
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36 |
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37 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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38 in the Department of Microbiology and Immunology at The University of Michigan, |
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39 provides bioinformatics for the microbial ecology community. |
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40 |
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41 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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42 |
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43 **Command Documenation** |
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44 |
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45 The mantel_ command calculates the Mantel correlation coefficient between two matrices_. |
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46 |
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47 .. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix |
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48 .. _mantel: http://www.mothur.org/wiki/Mantel |
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49 |
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50 |
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51 </help> |
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52 </tool> |