Mercurial > repos > iuc > mothur_cluster

annotate cluster.xml @ 0:5d1b3989db21 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 16:26:41 -0400
parents
children c212b5d35bfe
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
5d1b3989db21 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_cluster" name="Cluster" version="@WRAPPER_VERSION@.0">
5d1b3989db21 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>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
5d1b3989db21 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"/>
5d1b3989db21 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"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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8 <command detect_errors="aggressive"><![CDATA[
5d1b3989db21 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
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 ln -s "$matrix.dist" matrix.dist.dat &&
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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11 ln -s "$matrix.name" matrix.name.dat &&
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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12 ln -s "$count" count.dat &&
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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13
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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14 echo 'cluster(
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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15 #if $matrix.format == "phylip":
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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16 phylip=matrix.dist.dat,
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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17 #else
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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18 column=matrix.dist.dat,
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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19 #end if
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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20 #if $matrix.name:
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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21 name=matrix.name.dat,
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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22 #end if
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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23 #if $count:
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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24 count=count.dat,
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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25 #end if
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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26 hard=$hard,
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 #if float($cutoff) > 0.0:
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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28 cutoff=$cutoff,
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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29 #end if
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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30 precision=$precision,
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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31 sim=$sim,
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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32 method=$method
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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33 )'
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 | sed 's/ //g' ## mothur trips over whitespace
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 | mothur
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 ]]></command>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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37 <inputs>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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38 <conditional name="matrix">
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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39 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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40 <option value="column">Pairwise Column Matrix</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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41 <option value="phylip">Phylip Distance Matrix</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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42 </param>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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43 <when value="column">
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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44 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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45 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 </when>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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47 <when value="phylip">
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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48 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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49 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 </when>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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51 </conditional>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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52 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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53 <param name="method" type="select" label="method - Select a Clustering Method" help="">
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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54 <option value="furthest">Furthest neighbor</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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55 <option value="nearest">Nearest neighbor</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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56 <option value="average" selected="true">Average neighbor</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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57 <option value="weighted">Weighted</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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58 </param>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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59 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0.0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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60 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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61 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 <option value="10">.1</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <option value="100" selected="true">.01</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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64 <option value="1000">.001</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <option value="10000">.0001</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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66 <option value="100000">.00001</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 <option value="1000000">.000001</option>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 </param>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 </inputs>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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71 <outputs>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 <expand macro="logfile-output"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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73 <data name="rabund" format="mothur.rabund" from_work_dir="matrix.dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <data name="sabund" format="mothur.sabund" from_work_dir="matrix.dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <data name="otulist" format="mothur.list" from_work_dir="matrix.dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 </outputs>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <tests>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 <test><!-- test with phylip input -->
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 <param name="format" value="phylip"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <param name="dist" value="amazon.dist"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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82 <output name="sabund" file="amazon.an.sabund" ftype="mothur.sabund"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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83 <output name="otulist" md5="a6bf2a6ef7950b3ee2aa5bff4a662b6d" ftype="mothur.list"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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84 <expand macro="logfile-test"/>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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85 </test>
5d1b3989db21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 <test><!-- test with column input -->
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87 <param name="format" value="column"/>
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88 <param name="dist" value="amazon.pair.dist"/>
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89 <param name="name" value="amazon.names"/>
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90 <output name="rabund" md5="ec88216404729d0f4a0463e50e60c9ad" ftype="mothur.rabund"/>
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91 <output name="sabund" md5="f2c714531430b98d8cdfd3497468eec2" ftype="mothur.sabund"/>
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92 <output name="otulist" md5="1769463ed0b6680babe5801bf9c0a85c" ftype="mothur.list"/>
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93 <expand macro="logfile-test"/>
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94 </test>
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95 </tests>
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96 <help>
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97 <![CDATA[
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98
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99 @MOTHUR_OVERVIEW@
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100
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101 **Command Documenation**
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102
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103 The cluster_ 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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104
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105 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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106 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
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107 .. _name: http://www.mothur.org/wiki/Name_file
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108 .. _list: http://www.mothur.org/wiki/List_file
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109 .. _rabund: http://www.mothur.org/wiki/Rabund_file
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110 .. _sabund: http://www.mothur.org/wiki/Sabund_file
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111 .. _cluster: http://www.mothur.org/wiki/Cluster
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112
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113 ]]>
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114 </help>
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115 <expand macro="citations"/>
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116 </tool>