Mercurial > repos > iuc > mothur_cluster_split

annotate cluster.split.xml @ 0:e56e12d98ac4 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 16:26:26 -0400
parents
children bfd4e6980f44
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0
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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diff changeset
1 <tool profile="16.07" id="mothur_cluster_split" name="Cluster.split" version="@WRAPPER_VERSION@.0">
e56e12d98ac4 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) splits large matrices</description>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
e56e12d98ac4 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>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
e56e12d98ac4 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"/>
e56e12d98ac4 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"/>
e56e12d98ac4 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[
e56e12d98ac4 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
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 ln -s "$count" count.dat &&
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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11 #if $splitby.splitmethod == "distance":
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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12 ln -s "$splitby.matrix.dist" splitby.matrix.dist.dat &&
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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13 ln -s "$splitby.matrix.name" splitby.matrix.name.dat &&
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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14 #elif $splitby.splitmethod == "classify":
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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15 ln -s "$splitby.dist" splitby.dist.dat &&
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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16 ln -s "$splitby.name" splitby.name.dat &&
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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17 ln -s "$splitby.taxonomy" splitby.taxonomy.dat &&
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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18 #elif $splitby.splitmethod == "fasta":
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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19 ln -s "$splitby.fasta" splitby.fasta.dat &&
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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20 ln -s "$splitby.name" splitby.name.dat &&
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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21 ln -s "$splitby.taxonomy" splitby.taxonomy.dat &&
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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22 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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24 echo 'cluster.split(
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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25 splitmethod=$splitby.splitmethod,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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26 #if $splitby.splitmethod == "distance":
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 #if $splitby.matrix.format == "column":
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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28 column=splitby.matrix.dist.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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29 name=splitby.matrix.name.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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30 #elif $splitby.matrix.format == "phylip":
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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31 phylip=splitby.matrix.dist.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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32 #if $splitby.matrix.name:
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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33 name=splitby.matrix.name.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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34 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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35 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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36 #elif $splitby.splitmethod == "classify":
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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37 column=splitby.dist.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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38 name=splitby.name.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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39 taxonomy=splitby.taxonomy.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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40 #if $splitby.taxlevel > 1:
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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41 taxlevel=$splitby.taxlevel,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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42 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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43 #elif $splitby.splitmethod == "fasta":
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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44 fasta=splitby.fasta.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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45 name=splitby.name.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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46 taxonomy=splitby.taxonomy.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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47 #if $splitby.taxlevel > 1:
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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48 taxlevel=$splitby.taxlevel,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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49 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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50 classic=$splitby.classic,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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51 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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52 #if $count:
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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53 count=count.dat,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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54 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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55 #if $method:
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 method=$method,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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57 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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58 #if float($cutoff) > 0.0:
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 cutoff=$cutoff,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 hard=$hard,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 #if $precision
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 precision=$precision,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 #end if
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 large=$large,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 cluster=$cluster,
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 processors='\${GALAXY_SLOTS:-8}'
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 )'
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 | sed 's/ //g' ## mothur trips over whitespace
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 | mothur
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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71 ]]></command>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 <inputs>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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73 <conditional name="splitby">
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <param name="splitmethod" type="select" label="Split by" help="">
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <option value="distance">Distance</option>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 <option value="classify">Classification</option>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <option value="fasta">Classification using fasta</option>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 </param>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 <when value="distance">
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <conditional name="matrix">
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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82 <option value="column">Pairwise Column Matrix</option>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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83 <option value="phylip">Phylip Distance Matrix</option>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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84 </param>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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85 <when value="column">
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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87 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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88 </when>
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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89 <when value="phylip">
e56e12d98ac4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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90 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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91 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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92 </when>
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93 </conditional>
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94 </when>
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95 <when value="classify">
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96 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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97 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
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98 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
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99 <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
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100 </when>
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101 <when value="fasta">
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102 <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences" help="must be aligned sequences (mothur.align)"/>
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103 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
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104 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
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105 <param name="taxlevel" type="integer" value="3" label="taxlevel - taxonomy level for split (default=3)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
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106 <param name="classic" type="boolean" checked="false" truevalue="true" falsevalue="false" label="classic - Use cluster.classic"/>
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107 </when>
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108 </conditional>
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109 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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110 <param name="method" type="select" label="method - Select a Clustering Method" help="">
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111 <option value="furthest">Furthest neighbor</option>
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112 <option value="nearest">Nearest neighbor</option>
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113 <option value="average" selected="true">Average neighbor</option>
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114 </param>
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115 <param name="cutoff" type="float" value="0.0" min="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.25"/>
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116 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding" help=""/>
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117 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
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118 <option value="10">.1</option>
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119 <option value="100" selected="true">.01</option>
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120 <option value="1000">.001</option>
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121 <option value="10000">.0001</option>
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122 <option value="100000">.00001</option>
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123 <option value="1000000">.000001</option>
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124 </param>
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125 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - distance matrix is too large to fit in RAM" help="If your job fails due to not enough memory error, set this to true to rerun"/>
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126 <param name="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="The cluster parameter allows you to indicate whether you want to run the clustering or just split the distance matrix, default=T"/>
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127 </inputs>
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128 <outputs>
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129 <expand macro="logfile-output"/>
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130 <data name="rabund" format="mothur.rabund" from_work_dir="splitby.*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
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131 <data name="sabund" format="mothur.sabund" from_work_dir="splitby.*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
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132 <data name="otulist" format="mothur.list" from_work_dir="splitby.*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
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133 <collection name="splitdist" type="list" label="${tool.name} on ${on_string}: split dist">
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134 <filter>not cluster</filter>
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135 <discover_datasets pattern=".*?\.column\.dist\.(?P&lt;designation&gt;.*)\.temp" format="mothur.dist"/>
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136 </collection>
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137 <collection name="splitnames" type="list" label="${tool.name} on ${on_string}: split names">
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138 <filter>not cluster</filter>
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139 <discover_datasets pattern=".*?\.names\.(?P&lt;designation&gt;.*)\.temp" format="mothur.names"/>
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140 </collection>
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141 <data name="splitfile" format="txt" from_work_dir="splitby.*.file" label="${tool.name} on ${on_string}: split.file">
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142 <filter>not cluster</filter>
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143 </data>
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144 </outputs>
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145 <tests>
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146 <test><!-- test with distance method -->
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147 <param name="splitmethod" value="distance"/>
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148 <param name="format" value="phylip"/>
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149 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
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150 <output name="otulist" md5="2613ef0a1805ba9de012a41e938d8947" ftype="mothur.list"/>
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151 <output name="rabund" md5="4df813ec2d51c373a846a82380c7a1f8" ftype="mothur.rabund"/>
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152 <output name="sabund" md5="8d6813a5e8d2ad426a0ee5fdd99f1a19" ftype="mothur.sabund"/>
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153 <expand macro="logfile-test"/>
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154 </test>
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155 <test><!-- test with cluster false -->
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156 <param name="splitmethod" value="distance"/>
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157 <param name="format" value="phylip"/>
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158 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
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159 <param name="cluster" value="false"/>
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160 <output name="splitfile" ftype="txt">
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161 <assert_contents>
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162 <has_text text="column"/>
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163 <has_text text="dist"/>
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164 <has_text text="names"/>
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165 <has_text text="temp"/>
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166 </assert_contents>
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167 </output>
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168 <output_collection name="splitnames" count="4">
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169 <element name="0" md5="27037eeb3e696888b24653d0996261cd" ftype="mothur.names"/>
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170 </output_collection>
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171 <output_collection name="splitdist" count="3">
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172 <element name="4" md5="f751aee00b598d3b6691d34f67dbc8d5" ftype="mothur.dist"/>
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173 </output_collection>
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174 <expand macro="logfile-test"/>
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175 </test>
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176 <test><!-- test with classify method -->
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177 <param name="splitmethod" value="classify"/>
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178 <param name="format" value="column"/>
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179 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
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180 <param name="name" value="amazon.names" ftype="mothur.names"/>
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181 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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182 <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/>
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183 <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/>
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184 <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/>
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185 <expand macro="logfile-test"/>
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186 </test>
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187 <test><!-- test with fasta -->
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188 <param name="splitmethod" value="fasta"/>
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189 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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190 <param name="name" value="amazon.align_head.names" ftype="mothur.names"/>
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191 <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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192 <param name="cutoff" value="9999"/>
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193 <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/>
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194 <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/>
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195 <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/>
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196 <expand macro="logfile-test"/>
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197 </test>
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198 </tests>
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199 <help>
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200 <![CDATA[
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201
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202 @MOTHUR_OVERVIEW@
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203
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204
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205 **Command Documenation**
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206
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207 The cluster.split_ command assign sequences to OTUs (Operational Taxonomy Unit).
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208
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209 .. _cluster.split: http://www.mothur.org/wiki/Cluster.split
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210
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211 v1.28.0: Upgraded to Mothur 1.33, introduced cluster boolean.
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212
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213 ]]>
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214 </help>
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215 <expand macro="citations"/>
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216 </tool>