Mercurial > repos > iuc > mothur_chimera_perseus
annotate chimera.perseus.xml @ 8:17df89a5847b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
author | iuc |
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date | Tue, 08 Dec 2020 14:34:25 +0000 |
parents | 128cbea05aeb |
children | 54bc4863eb3d |
rev | line source |
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35c11001da8b
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_chimera_perseus" name="Chimera.perseus" version="@WRAPPER_VERSION@.0"> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Find putative chimeras using chimeraCheck</description> |
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3 <macros> |
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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> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/> |
35c11001da8b
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"/> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[ |
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1dab91d5c40e
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10 @SHELL_OPTIONS@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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11 |
2
1dab91d5c40e
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 |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$fasta' fasta.dat && |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$name' name.dat && |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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15 ln -s '$group' group.dat && |
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35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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16 |
2
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 echo 'chimera.perseus( |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 fasta=fasta.dat, |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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19 #if $name.is_of_type("mothur.names"): |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 name=name.dat, |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 #elif $name.is_of_type("mothur.count_table"): |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 count=name.dat, |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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24 #if $group: |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 group=group.dat, |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 #end if |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 alpha=$alpha, |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 beta=$beta, |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 cutoff=$cutoff, |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 dereplicate=$dereplicate, |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 processors='\${GALAXY_SLOTS:-8}' |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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32 )' |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 | sed 's/ //g' ## mothur trips over whitespace |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 | mothur |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 | tee mothur.out.log |
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35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 ]]></command> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <inputs> |
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1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 <param argument="fasta" type="data" format="mothur.align" label="fasta - Candiate Aligned Sequences"/> |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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39 <param argument="name" type="data" format="mothur.names,mothur.count_table" label="name - Names or count_table"/> |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 <param argument="alpha" type="float" value="-5.54" label="alpha" help="The default is -5.54"/> |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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42 <param argument="beta" type="float" value="0.33" label="beta" help="The default is 0.33"/> |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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43 <param argument="cutoff" type="float" value="0.50" label="cutoff" help="The default is 0.50"/> |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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44 <param argument="dereplicate" type="boolean" falsevalue="false" truevalue="true" checked="false" label="dereplicate - remove chimeric sequences from all groups" |
1dab91d5c40e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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45 help="If parameter is false, then if one group finds the seqeunce to be chimeric, then all groups find it to be chimeric. default=false"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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46 <expand macro="param-savelog"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 <expand macro="logfile-output"/> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 <data name="out_chimeras" format="tabular" from_work_dir="fasta.perseus.chimeras" label="${tool.name} on ${on_string}: perseus.chimeras"/> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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51 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.perseus.accnos" label="${tool.name} on ${on_string}: perseus.accnos"/> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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52 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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54 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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55 <param name="fasta" value="amazon.fasta" ftype="fasta"/> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 <param name="name" value="amazon1.names" ftype="mothur.names"/> |
35c11001da8b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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57 <output name="out_chimeras" md5="bcd513127321a32035764a2087c23528" ftype="tabular"/> |
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1dab91d5c40e
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58 <param name="savelog" value="true"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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59 <expand macro="logfile-test"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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60 </test> |
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61 <!-- TODO: find/create test dataset with chimera present --> |
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62 </tests> |
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63 <help><![CDATA[ |
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64 |
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65 @MOTHUR_OVERVIEW@ |
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66 |
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67 **Command Documentation** |
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68 |
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69 The chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences. |
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70 |
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71 .. _chimera.perseus: https://www.mothur.org/wiki/Chimera.perseus |
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72 |
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73 ]]></help> |
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74 <expand macro="citations"> |
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75 <citation type="doi">10.1186/1471-2105-12-38</citation> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a
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76 </expand> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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changeset
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77 </tool> |