Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/pcoa.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
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1 <tool id="mothur_pcoa" name="Pcoa" version="1.20.0" > |
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2 <description>Principal Coordinate Analysis for a distance matrix</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='pcoa' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pcoa\.axes$:'$pcoa,'^\S+\.pcoa.loadings$:'$loadings |
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7 --outputdir='$logfile.extra_files_path' |
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8 --phylip=$phylip |
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9 $metric |
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10 </command> |
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11 <inputs> |
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12 <param name="phylip" type="data" format="lower.dist,square.dist" label="phylip - Phylip Distance Matrix"/> |
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13 <param name="metric" type="boolean" truevalue="" falsevalue="--metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" /> |
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14 </inputs> |
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15 <outputs> |
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16 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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17 <data format="axes" name="pcoa" label="${tool.name} on ${on_string}: pcoa.axes" /> |
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18 <data format="tabular" name="loadings" label="${tool.name} on ${on_string}: loadings" /> |
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19 </outputs> |
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20 <requirements> |
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21 <requirement type="package" version="1.33">mothur</requirement> |
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22 </requirements> |
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23 <tests> |
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24 </tests> |
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25 <help> |
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26 **Mothur Overview** |
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27 |
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28 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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29 in the Department of Microbiology and Immunology at The University of Michigan, |
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30 provides bioinformatics for the microbial ecology community. |
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31 |
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32 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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33 |
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34 **Command Documenation** |
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35 |
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36 The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_. |
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37 |
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38 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix |
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39 .. _pcoa: http://www.mothur.org/wiki/Pcoa |
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40 |
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41 </help> |
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42 </tool> |