Mercurial > repos > iuc > mothur_pcoa

annotate pcoa.xml @ 10:40b0d8eb3725 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:39:45 +0000
parents c9fc98593dec
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1 <tool profile="16.07" id="mothur_pcoa" name="Pcoa" version="@WRAPPER_VERSION@.0">
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2 <description>Principal Coordinate Analysis for a distance matrix</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
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11 @SHELL_OPTIONS@
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12
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13 ## create symlinks to input datasets
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14 ln -s '$phylip' phylip.dat &&
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16 echo 'pcoa(
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17 phylip=phylip.dat,
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18 metric=$metric
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19 )'
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20 | sed 's/ //g' ## mothur trips over whitespace
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21 | mothur
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22 | tee mothur.out.log
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23 ]]></command>
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24 <inputs>
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25 <param name="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/>
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26 <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
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27 <expand macro="param-savelog"/>
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28 </inputs>
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29 <outputs>
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30 <expand macro="logfile-output"/>
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31 <data name="pcoa" format="mothur.axes" from_work_dir="phylip*.pcoa.axes" label="${tool.name} on ${on_string}: pcoa.axes"/>
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32 <data name="loadings" format="tabular" from_work_dir="phylip*.pcoa.loadings" label="${tool.name} on ${on_string}: loadings"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="phylip" value="amazon.dist"/>
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37 <output name="pcoa" file="amazon.pcoa.axes"/>
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38 <output name="loadings" file="amazon.pcoa.loadings"/>
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39 <param name="savelog" value="true"/>
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40 <expand macro="logfile-test"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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45 @MOTHUR_OVERVIEW@
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46
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47 **Command Documentation**
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48
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49 The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_.
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50
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51 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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52 .. _pcoa: https://www.mothur.org/wiki/Pcoa
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54 ]]></help>
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55 <expand macro="citations">
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56 <expand macro="citations-ecology"/>
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57 </expand>
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58 </tool>