Mercurial > repos > iuc > mothur_hcluster

annotate hcluster.xml @ 0:e5faf9bdcbbe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:35:04 -0400
parents
children db21b211d44c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_hcluster" name="Hcluster" version="@WRAPPER_VERSION@.0">
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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6 <expand macro="requirements"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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7 <expand macro="version_command"/>
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iuc
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8 <command detect_errors="aggressive"><![CDATA[
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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9 ## create symlinks to input datasets
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 ln -s "$matrix.dist" matrix.dist.dat &&
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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11 ln -s "$matrix.name" matrix.name.dat &&
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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13 echo 'hcluster(
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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14 #if $matrix.format == "column":
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 column=matrix.dist.dat,
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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16 name=matrix.name.dat,
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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17 #elif $matrix.format == "phylip":
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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18 phylip=matrix.dist.dat,
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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19 #if $matrix.name:
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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20 name=matrix.name.dat,
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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21 #end if
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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22 #end if
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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23 method=$method,
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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24 #if $cutoff:
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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25 cutoff=$cutoff,
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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26 #end if
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 precision=$precision,
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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28 hard=$hard,
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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29 sorted=$sorted,
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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30 showabund=$showabund
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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31 )'
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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32 | sed 's/ //g' ## mothur trips over whitespace
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 | mothur
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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34 ]]></command>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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35 <inputs>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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36 <conditional name="matrix">
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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37 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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38 <option value="column">Pairwise Column Matrix</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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39 <option value="phylip">Phylip Distance Matrix</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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40 </param>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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41 <when value="column">
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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42 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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43 <param name="name" type="data" format="mothur.names" label="name - Names"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 </when>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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45 <when value="phylip">
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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46 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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47 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 </when>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 </conditional>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <param name="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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51 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 <option value="10">.1</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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54 <option value="100" selected="true">.01</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 <option value="1000">.001</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <option value="10000">.0001</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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57 <option value="100000">.00001</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <option value="1000000">.000001</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 </param>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <param name="method" type="select" label="method - Select a Clustering Method" help="">
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 <option value="average" selected="true">Average neighbor</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 <option value="nearest">Nearest neighbor</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <option value="furthest">Furthest neighbor</option>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 <option value="weighted">Weighted</option>
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65 </param>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - The input matrix is already sorted"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 <param name="showabund" type="boolean" checked="true" truevalue="true" falsevalue="false" label="showabund - Verbose ouput"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 </inputs>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 <outputs>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 <expand macro="logfile-output"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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71 <data name="rabund" format="mothur.rabund" from_work_dir="matrix.dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 <data name="sabund" format="mothur.sabund" from_work_dir="matrix.dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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73 <data name="otulist" format="mothur.list" from_work_dir="matrix.dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 </outputs>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <tests>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 <test><!-- test with phylip input-->
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <param name="format" value="phylip"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 <param name="dist" value="98_sq_phylip_amazon.dist"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 <output name="rabund" md5="aafe1357a2f76e2d05e52c5a26838061" ftype="mothur.rabund"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <output name="sabund" md5="103af393a98579aec05e3cc935343a3c" ftype="mothur.sabund"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <output name="otulist" ftype="mothur.list">
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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82 <assert_contents>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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83 <has_text text="unique"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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84 <has_text text="label"/>
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85 <has_text text="numOtus"/>
e5faf9bdcbbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 <has_text text="Otu98"/>
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87 </assert_contents>
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88 </output>
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89 <expand macro="logfile-test"/>
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90 </test>
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91 <test><!-- test with column and name input -->
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92 <param name="format" value="column"/>
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93 <param name="dist" value="amazon.pair.dist"/>
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94 <param name="name" value="amazon.names"/>
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95 <output name="rabund" md5="ec88216404729d0f4a0463e50e60c9ad" ftype="mothur.rabund"/>
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96 <output name="sabund" md5="f2c714531430b98d8cdfd3497468eec2" ftype="mothur.sabund"/>
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97 <output name="otulist" ftype="mothur.list">
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98 <assert_contents>
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99 <has_text text="unique"/>
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100 <has_text text="label"/>
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101 <has_text text="numOtus"/>
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102 <has_text text="Otu96"/>
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103 </assert_contents>
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104 </output>
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105 <expand macro="logfile-test"/>
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106 </test>
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107 </tests>
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108 <help>
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109 <![CDATA[
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110
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111 @MOTHUR_OVERVIEW@
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112
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113 **Command Documenation**
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114
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115 The hcluster_ command assign sequences to OTUs (Operational Taxonomy Unit). The assignment is based on a phylip-formatted_distance_matrix_ or a column-formatted_distance_matrix_ and name_ file. It generates a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
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116
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117 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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118 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
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119 .. _name: http://www.mothur.org/wiki/Name_file
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120 .. _list: http://www.mothur.org/wiki/List_file
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121 .. _rabund: http://www.mothur.org/wiki/Rabund_file
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122 .. _sabund: http://www.mothur.org/wiki/Sabund_file
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123 .. _hcluster: http://www.mothur.org/wiki/Hcluster
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124
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125 ]]>
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126 </help>
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127 <expand macro="citations"/>
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128 </tool>