Mercurial > repos > iuc > mothur_split_abund

annotate split.abund.xml @ 2:407a5352f0ec 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 22:01:54 -0400
parents b15d9a2d2311
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b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_split_abund" name="Split.abund" version="@WRAPPER_VERSION@.0">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Separate sequences into rare and abundant groups</description>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
2
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@
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b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
2
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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12 ## create symlinks to input datasets
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$fasta' fasta.dat &&
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$search.input' search_input.dat &&
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 #if $split.dosplit == "yes":
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 ln -s '$split.group' split_group.dat &&
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 #end if
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b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18
2
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 echo 'split.abund(
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 fasta=fasta.dat,
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #if $search.type == "list":
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 list=search_input.dat,
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 #if $search.label:
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 label=${ str($search.label).replace(",","-") },
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #end if
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #elif $search.type == "name":
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 name=search_input.dat,
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 #else
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 count=search_input.dat,
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 #end if
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 #if $split.dosplit == "yes":
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 #if $split.group:
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 group=split_group.dat,
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 #end if
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 #if $split.groups:
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 groups=${ str($split.groups).replace(",","-") },
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 #end if
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 #end if
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 accnos=$accnos,
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 cutoff=$cutoff
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 )'
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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42 | sed 's/ //g' ## mothur trips over whitespace
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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43 | mothur
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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44 | tee mothur.out.log
0
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 ]]></command>
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46 <inputs>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 <conditional name="search">
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50 <param name="type" type="select" label="Type to screen" help="">
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51 <option value="list">OTU List</option>
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52 <option value="name">Name reference</option>
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53 <option value="count">Count file</option>
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54 </param>
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55 <when value="name">
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56 <param name="input" type="data" format="mothur.names" label="name - Name reference"/>
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57 </when>
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58 <when value="list">
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59 <param name="input" type="data" format="mothur.list" label="list - OTU List"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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60 <param name="label" type="select" label="label - OTU Labels" multiple="true" help="Select OTU Labels to filter out all but selected labels">
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61 <options>
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62 <filter type="data_meta" ref="input" key="labels"/>
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63 </options>
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64 </param>
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65 </when>
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66 <when value="count">
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67 <param name="input" type="data" format="mothur.count_table" label="count - count_table file"/>
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68 </when>
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69 </conditional>
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70 <conditional name="split">
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71 <param name="dosplit" type="select" label="Parse a group file into abundant and rare groups? (only possible if name or list file supplied)" help="">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 <option value="no" selected="true">No</option>
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73 <option value="yes">Yes</option>
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74 </param>
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75 <when value="yes">
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76 <param name="group" type="data" format="mothur.groups" label="group - Group dataset"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 <param name="groups" type="select" multiple="true" label="groups - Group Selection">
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78 <options>
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79 <filter type="data_meta" ref="group" key="groups"/>
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80 </options>
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81 </param>
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82 </when>
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83 <when value="no"/>
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84 </conditional>
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85 <param name="accnos" type="boolean" truevalue="true" falsevalue="false" checked="false" label="accnos - Produce rare and abundant Accession outputs"/>
2
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
86 <expand macro="param-savelog"/>
0
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
87 </inputs>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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88 <outputs>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
89 <expand macro="logfile-output"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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90 <data name="abund_fasta" format_source="fasta" from_work_dir="*abund.fasta" label="${tool.name} on ${on_string}: abund.fasta">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
91 <filter>search['type'] != 'list'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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92 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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93 <data name="rare_fasta" format_source="fasta" from_work_dir="*rare.fasta" label="${tool.name} on ${on_string}: rare.fasta">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
94 <filter>search['type'] != 'list'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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95 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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96 <data name="abund_groups" format="mothur.groups" label="${tool.name} on ${on_string}: abund.groups">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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97 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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98 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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99 <data name="rare_groups" format="mothur.groups" label="${tool.name} on ${on_string}: rare.groups">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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100 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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101 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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102 <data name="abund_names" format="mothur.names" from_work_dir="search_input*.abund.names" label="${tool.name} on ${on_string}: abund.names">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
103 <filter>search['type'] == 'name'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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104 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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105 <data name="rare_names" format="mothur.names" from_work_dir="search_input*.rare.names" label="${tool.name} on ${on_string}: rare.fasta">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
106 <filter>search['type'] == 'name'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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107 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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108 <data name="abund_count" format="mothur.count_table" from_work_dir="*.abund.count_table" label="${tool.name} on ${on_string}: abund.count_table">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
109 <filter>search['type'] == 'count'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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110 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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111 <data name="rare_count" format="mothur.count_table" from_work_dir="*.rare.count_table" label="${tool.name} on ${on_string}: rare.count_table">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
112 <filter>search['type'] == 'count'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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113 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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114 <data name="abund_accnos" format="mothur.accnos" from_work_dir="*abund.accnos" label="${tool.name} on ${on_string}: abund.accnos">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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115 <filter>search['type'] != 'list' and accnos</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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116 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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117 <data name="rare_accnos" format="mothur.accnos" from_work_dir="*rare.accnos" label="${tool.name} on ${on_string}: rare.accnos">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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118 <filter>search['type'] != 'list' and accnos</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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119 </data>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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120 <collection name="abund_fasta_coll" type="list" label="${tool.name} on ${on_string}: abund.fasta">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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121 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.fasta" format="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
122 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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123 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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124 <collection name="rare_fasta_coll" type="list" label="${tool.name} on ${on_string}: rare.fasta">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
125 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.fasta" format="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
126 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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127 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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128 <collection name="abund_list_coll" type="list" label="${tool.name} on ${on_string}: abund.list">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
129 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.list" format="mothur.list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
130 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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131 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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132 <collection name="rare_list_coll" type="list" label="${tool.name} on ${on_string}: rare.list">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
133 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.list" format="mothur.list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
134 <filter>search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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135 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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136 <collection name="abund_accnos_coll" type="list" label="${tool.name} on ${on_string}: abund.accnos">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
137 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.accnos" format="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
138 <filter>(search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')) and accnos</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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139 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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140 <collection name="rare_accnos_coll" type="list" label="${tool.name} on ${on_string}: rare.accnos">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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141 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.accnos" format="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
142 <filter>(search['type'] == 'list' or (search['type'] == 'name' and split['dosplit'] == 'yes')) and accnos</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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143 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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144 <collection name="abund_groups_coll" type="list" label="${tool.name} on ${on_string}: abund.groups">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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145 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.groups" format="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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146 <filter>search['type'] != 'count' and split['dosplit'] == 'yes'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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147 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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148 <collection name="rare_groups_coll" type="list" label="${tool.name} on ${on_string}: rare.groups">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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149 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.groups" format="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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150 <filter>search['type'] != 'count' and split['dosplit'] == 'yes'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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151 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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152 <collection name="abund_names_coll" type="list" label="${tool.name} on ${on_string}: abund.names">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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153 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.abund\.names" format="mothur.names"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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154 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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155 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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156 <collection name="rare_names_coll" type="list" label="${tool.name} on ${on_string}: rare.names">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
157 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rare\.names" format="mothur.names"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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158 <filter>search['type'] == 'name' and split['dosplit'] == 'yes'</filter>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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159 </collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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diff changeset
160 </outputs>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
161 <tests>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
162 <test><!-- test with count table -->
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
163 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
164 <param name="type" value="count"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
165 <param name="input" value="amazon.count_table" ftype="mothur.count_table"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
166 <param name="cutoff" value="1"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
167 <param name="accnos" value="true"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
168 <output name="abund_fasta" md5="3c147ce7224bc8c8602d2ccfe4b6eae7" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
169 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
170 <output name="abund_count" md5="288e5222f3d454b67761fca3c8c944b1" ftype="mothur.count_table"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
171 <output name="rare_count" md5="dc7be856861ef53faa73a5312b0661c3" ftype="mothur.count_table"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
172 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
173 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
2
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
174 <param name="savelog" value="true"/>
0
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
175 <expand macro="logfile-test"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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176 </test>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
177 <test><!-- test with name file and accnos output -->
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
178 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
179 <param name="type" value="name"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
180 <param name="input" value="amazon.names" ftype="mothur.names"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
181 <param name="cutoff" value="1"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
182 <param name="accnos" value="true"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
183 <output name="abund_fasta" md5="3c147ce7224bc8c8602d2ccfe4b6eae7" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
184 <output name="rare_fasta" md5="bff57d4585fe4e6d8b86c949f3e17e1a" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
185 <output name="abund_names" md5="41560e422d53c83cb482ef868409136c" ftype="mothur.names"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
186 <output name="rare_names" md5="12527477b2c1891c9278f417a5ece45d" ftype="mothur.names"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
187 <output name="abund_accnos" md5="47c918c965d41fea12bad748afe60833" ftype="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
188 <output name="rare_accnos" md5="3537f34f96d276e72e03f6d6a4994fd9" ftype="mothur.accnos"/>
2
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
189 <param name="savelog" value="true"/>
0
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
190 <expand macro="logfile-test"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
191 </test>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
192 <test><!-- test with name file and accnos output with groups-->
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
193 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
194 <param name="type" value="name"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
195 <param name="input" value="amazon.names" ftype="mothur.names"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
196 <param name="cutoff" value="1"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
197 <param name="accnos" value="true"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
198 <param name="dosplit" value="yes"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
199 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
200 <param name="groups" value="forest,pasture"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
201 <output_collection name="abund_fasta_coll" count="2">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
202 <element name="forest" md5="8d90da3c099450e31de006548e8f458c" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
203 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
204 <output_collection name="rare_fasta_coll" count="2">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
205 <element name="forest" md5="4459f7ee4c46ccf0ce33f5694ac1ca49" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
206 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
207 <output_collection name="abund_names_coll" count="2">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
208 <element name="pasture" md5="d45b69987a0294c87fab358bbb71cd29" ftype="mothur.names"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
209 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
210 <output_collection name="rare_names_coll" count="2">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
211 <element name="pasture" md5="fc5d939ceca270be00b39d5323c1a79f" ftype="mothur.names"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
212 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
213 <output_collection name="abund_accnos_coll" count="2">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
214 <element name="forest" md5="597a2cc6d2da897434ec9d2c11489d0a" ftype="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
215 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
216 <output_collection name="rare_accnos_coll" count="2">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
217 <element name="forest" md5="20f8e54d68bf225f405258942e0cb5ac" ftype="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
218 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
219 <output_collection name="abund_groups_coll" count="2">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
220 <element name="pasture" md5="46ac8394df6b3376b41619b07720ee18" ftype="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
221 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
222 <output_collection name="rare_groups_coll" count="2">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
223 <element name="pasture" md5="5907bd7fe874a29fcc57930ecb0f65d1" ftype="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
224 </output_collection>
2
407a5352f0ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 0
diff changeset
225 <param name="savelog" value="true"/>
0
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
226 <expand macro="logfile-test"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
227 </test>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
228 <test><!-- test with list -->
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
229 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
230 <param name="type" value="list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
231 <param name="input" value="amazon.an.list" ftype="mothur.list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
232 <param name="cutoff" value="2"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
233 <param name="accnos" value="true"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
234 <param name="dosplit" value="yes"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
235 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
236 <param name="groups" value="forest,pasture"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
237 <output_collection name="abund_fasta_coll" count="72">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
238 <element name="0.05.forest" md5="1860c0cf143a2b7adc93c88418ed3559" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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239 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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240 <output_collection name="rare_fasta_coll" count="72">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
241 <element name="0.05.pasture" md5="7c9ca6c2f3e2eb5c3d38c30963b3d976" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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242 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
243 <output_collection name="abund_list_coll" count="72">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
244 <element name="forest.0.05" md5="8a0843911399171a73afbc0374065fd0" ftype="mothur.list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
245 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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246 <output_collection name="rare_list_coll" count="72">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
247 <element name="pasture.0.05" md5="b7dc64a835d318852dbadc0c3379d0bb" ftype="mothur.list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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248 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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249 <output_collection name="abund_accnos_coll" count="72">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
250 <element name="0.05.forest" md5="e9f9b640ca00c11cba5420069c916b12" ftype="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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251 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
252 <output_collection name="rare_accnos_coll" count="72">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
253 <element name="0.05.pasture" md5="e866c488171950bb38e7ba4c8f2982c1" ftype="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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254 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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255 <output_collection name="abund_groups_coll" count="72">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
256 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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257 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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258 <output_collection name="rare_groups_coll" count="72">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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259 <element name="0.05.pasture" md5="ddcf8bc26a0815fd366deceec64133ee" ftype="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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260 </output_collection>
2
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261 <param name="savelog" value="true"/>
0
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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262 <expand macro="logfile-test"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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263 </test>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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264 <test><!-- test with list and label and group select-->
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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265 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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266 <param name="type" value="list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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267 <param name="input" value="amazon.an.list" ftype="mothur.list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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268 <param name="cutoff" value="2"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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269 <param name="label" value="0.05,0.22"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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270 <param name="accnos" value="true"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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271 <param name="dosplit" value="yes"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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272 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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273 <param name="groups" value="forest,pasture"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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274 <output_collection name="abund_fasta_coll" count="4">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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275 <element name="0.05.pasture" md5="51327cbf0c66c9c3074ca3456b021ead" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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276 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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277 <output_collection name="rare_fasta_coll" count="4">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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278 <element name="0.05.pasture" md5="7c9ca6c2f3e2eb5c3d38c30963b3d976" ftype="fasta"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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279 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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280 <output_collection name="abund_list_coll" count="4">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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281 <element name="forest.0.05" md5="8a0843911399171a73afbc0374065fd0" ftype="mothur.list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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282 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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283 <output_collection name="rare_list_coll" count="4">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
284 <element name="forest.0.05" md5="f79b02e37dbd7a7f76a60c269571396f" ftype="mothur.list"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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285 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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286 <output_collection name="abund_accnos_coll" count="4">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
287 <element name="0.05.pasture" md5="3a875836ffebfeb037cd761ea1d0607e" ftype="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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288 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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289 <output_collection name="rare_accnos_coll" count="4">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
290 <element name="0.05.pasture" md5="e866c488171950bb38e7ba4c8f2982c1" ftype="mothur.accnos"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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291 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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292 <output_collection name="abund_groups_coll" count="4">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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293 <element name="0.05.forest" md5="fd404451b15195cadb637751a463a077" ftype="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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294 </output_collection>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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295 <output_collection name="rare_groups_coll" count="4">
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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296 <element name="0.05.forest" md5="53a2f24a4d69f92661b94bc4b813ce69" ftype="mothur.groups"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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297 </output_collection>
2
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298 <param name="savelog" value="true"/>
0
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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299 <expand macro="logfile-test"/>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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300 </test>
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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301 </tests>
2
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302 <help><![CDATA[
0
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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303
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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304 @MOTHUR_OVERVIEW@
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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305
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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306 **Command Documentation**
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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307
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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308 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups.
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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309
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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310 .. _list: https://www.mothur.org/wiki/List_file
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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311 .. _name: https://www.mothur.org/wiki/Name_file
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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312 .. _split.abund: https://www.mothur.org/wiki/Split.abund
2
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313
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diff changeset
314 ]]></help>
0
b15d9a2d2311 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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315 <expand macro="citations"/>
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316 </tool>