Mercurial > repos > iuc > mothur_venn

annotate venn.xml @ 2:8bfc093999ff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:03:29 -0400
parents af481cd93ede
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_venn" name="Venn" version="@WRAPPER_VERSION@.0">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>Generate Venn diagrams for groups </description>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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5 </macros>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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6 <expand macro="requirements"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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7 <expand macro="stdio"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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8 <expand macro="version_command"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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9 <command><![CDATA[
2
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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10 @SHELL_OPTIONS@
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af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
2
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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12 ## create symlinks to input datasets
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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13 ln -s '$input.otu' input_otu.dat &&
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af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14
2
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 echo 'venn(
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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16 #if $input.source == "shared":
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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17 shared=input_otu.dat,
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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18 nseqs=$nseqs,
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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19 permute=$permute,
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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20 #if $input.groups:
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
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21 groups=${ str($input.groups).replace(",","-") },
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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22 #end if
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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23 #elif $input.source == "similarity":
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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24 list=input_otu.dat,
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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25 abund=$input.abund,
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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26 #end if
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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27 #if $input.label:
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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28 label=${ str($input.label).replace(",","-") },
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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29 #end if
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 #if $input.calc:
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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31 calc=${ str($input.calc).replace(",","-") },
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 #end if
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 fontsize=$fontsize,
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 sharedotus=$sharedotus
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 )'
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 | sed 's/ //g' ## mothur trips over whitespace
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 | mothur
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 | tee mothur.out.log
0
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 ]]></command>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <inputs>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 <conditional name="input">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 <param name="source" type="select" label="Generate Heatmap for">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 <option value="shared">OTU Shared</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 <option value="similarity">OTU list</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 </param>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 <when value="shared">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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47 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 <option value="sharedsobs">Shared Sobs</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 <option value="sharedchao">Shared Chao</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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51 <option value="sharedace">Shared Ace</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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52 </param>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 <param name="label" type="select" multiple="true" label="label - OTU Labels">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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54 <expand macro="labeloptions"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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55 </param>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 <param name="groups" type="select" multiple="true" label="groups - Groups to consider">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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57 <options>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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58 <filter type="data_meta" ref="otu" key="groups"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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59 </options>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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60 </param>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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61 </when>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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62 <when value="similarity">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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63 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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64 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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65 <option value="sobs">Sobs</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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66 <option value="chao">Chao</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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67 <option value="ace">Ace</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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68 </param>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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69 <param name="abund" type="integer" value="10" min="5" label="abund - Abundance when using the ace calculator ( >= 5 )"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 <param name="label" type="select" multiple="true" label="label - OTU Labels">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 <expand macro="labeloptions"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 </param>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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73 </when>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 </conditional>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <param name="nseqs" type="boolean" falsevalue="false" truevalue="true" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 <param name="permute" type="select" label="permute - Create pictures with all possible 4-way permutations of groups">
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 <option value="1">1</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 <option value="2">2</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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79 <option value="3">3</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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80 <option value="4" selected="true">4</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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81 <option value="true">true</option>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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82 </param>
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83 <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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84 <param name="sharedotus" type="boolean" falsevalue="false" truevalue="true" checked="true" label="sharedotus - This parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=T"/>
2
8bfc093999ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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85 <expand macro="param-savelog"/>
0
af481cd93ede planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 </inputs>
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87 <outputs>
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88 <collection name="sharedotus_out" type="list" label="${tool.name} on ${on_string}: sharedotus">
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89 <filter>sharedotus</filter>
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90 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.sharedotus" format="tabular"/>
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91 </collection>
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92 <collection name="svgs_out" type="list" label="${tool.name} on ${on_string}: svg">
2
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93 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.svg" format="svg"/>
0
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94 </collection>
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95 <expand macro="logfile-output"/>
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96 </outputs>
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97 <tests>
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98 <test><!-- test with shared file -->
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99 <param name="source" value="shared"/>
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100 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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101 <param name="calc" value="sharedsobs,sharedchao"/>
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102 <param name="groups" value="forest,pasture"/>
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103 <output_collection name="sharedotus_out" count="35">
2
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104 <element name="0.05.sharedsobs.forest-pasture" md5="7513c9df64477a08b69f0d4665011e80" ftype="tabular" />
0
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105 </output_collection>
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106 <output_collection name="svgs_out" count="72">
2
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107 <element name="0.05.sharedsobs.forest-pasture" md5="e2dc0d5485520f5b22aa185ba91b123e" ftype="svg" />
0
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108 </output_collection>
2
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109 <param name="savelog" value="true"/>
0
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110 <expand macro="logfile-test"/>
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111 </test>
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112 <test><!-- test with list file -->
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113 <param name="source" value="similarity"/>
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114 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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115 <param name="calc" value="sobs,chao,ace"/>
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116 <param name="groups" value="forest,pasture"/>
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117 <output_collection name="svgs_out" count="108">
2
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118 <element name=".0.45.ace" md5="d69778f507939bc2f5d2bbc3a0088f21" ftype="svg"/>
0
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119 </output_collection>
2
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120 <param name="savelog" value="true"/>
0
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121 <expand macro="logfile-test"/>
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122 </test>
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123 </tests>
2
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124 <help><![CDATA[
0
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125
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126 @MOTHUR_OVERVIEW@
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127
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128 **Command Documentation**
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129
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130 The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
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131
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132 .. _venn: https://www.mothur.org/wiki/Venn
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133
2
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134 ]]></help>
0
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135 <expand macro="citations"/>
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136 </tool>