Mercurial > repos > iuc > mothur_pcoa

annotate pcoa.xml @ 3:bda98cd0280d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:18:47 -0500
parents 1db0331b2861
children 4324f5db21cc
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3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_pcoa" name="Pcoa" version="@WRAPPER_VERSION@.0">
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Principal Coordinate Analysis for a distance matrix</description>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
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4 <import>macros.xml</import>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
bda98cd0280d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$phylip' phylip.dat &&
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15 echo 'pcoa(
bda98cd0280d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 phylip=phylip.dat,
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17 metric=$metric
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18 )'
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19 | sed 's/ //g' ## mothur trips over whitespace
bda98cd0280d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 | mothur
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21 | tee mothur.out.log
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22 ]]></command>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 <inputs>
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24 <param name="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/>
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25 <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 </inputs>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 <outputs>
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28 <expand macro="logfile-output"/>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 <data name="pcoa" format="mothur.axes" from_work_dir="phylip*.pcoa.axes" label="${tool.name} on ${on_string}: pcoa.axes"/>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 <data name="loadings" format="tabular" from_work_dir="phylip*.pcoa.loadings" label="${tool.name} on ${on_string}: loadings"/>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 </outputs>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <tests>
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33 <test>
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34 <param name="phylip" value="amazon.dist"/>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <output name="pcoa" file="amazon.pcoa.axes"/>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <output name="loadings" file="amazon.pcoa.loadings"/>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <expand macro="logfile-test"/>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 </test>
3c45088895b5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 </tests>
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40 <help><![CDATA[
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42 @MOTHUR_OVERVIEW@
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43
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44 **Command Documentation**
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46 The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_.
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47
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48 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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49 .. _pcoa: https://www.mothur.org/wiki/Pcoa
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51 ]]></help>
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52 <expand macro="citations"/>
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53 </tool>