Mercurial > repos > iuc > mothur_get_otus
annotate get.otus.xml @ 3:009304a59939 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author | iuc |
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date | Fri, 06 Apr 2018 04:17:37 -0400 |
parents | 04a479ceb84a |
children | 3f68e8e700c9 |
rev | line source |
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0
a1aea42f0f8e
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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1 <tool profile="16.07" id="mothur_get_otus" name="Get.otus" version="@WRAPPER_VERSION@.0"> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>Get otus containing sequences from specified groups</description> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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4 <import>macros.xml</import> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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5 </macros> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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6 <expand macro="requirements"/> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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7 <expand macro="stdio"/> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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8 <expand macro="version_command"/> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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9 <command><![CDATA[ |
2
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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10 @SHELL_OPTIONS@ |
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a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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11 |
2
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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12 ## create symlinks to input datasets |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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13 ln -s '$accnos' accnos.dat && |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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14 #if $list: |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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15 ln -s '$list' list.dat && |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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16 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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17 #if $shared: |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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18 ln -s '$shared' shared.dat && |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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19 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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20 #if $constaxonomy: |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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21 ln -s '$constaxonomy' constaxonomy.dat && |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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22 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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23 #if $corraxes: |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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24 ln -s '$corraxes' corraxes.dat && |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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25 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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26 #if $otucorr: |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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27 ln -s '$otucorr' otucorr.dat && |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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28 #end if |
0
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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29 |
2
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 echo 'get.otus( |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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31 #if $list |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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32 list=list.dat, |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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33 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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34 #if $shared |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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35 shared=shared.dat, |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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36 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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37 #if $corraxes: |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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38 corraxes=corraxes.dat, |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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39 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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40 #if $otucorr: |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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41 otucorr=otucorr.dat, |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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42 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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43 #if $constaxonomy |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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44 constaxonomy=constaxonomy.dat, |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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45 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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46 accnos=accnos.dat |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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47 #if $labelsource.label: |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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48 ,label=${ str($labelsource.label).replace(",","-") } |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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49 #end if |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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50 )' |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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51 | sed 's/ //g' ## mothur trips over whitespace |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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52 | mothur |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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53 | tee mothur.out.log |
0
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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54 ]]></command> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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55 <inputs> |
2
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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56 <param argument="accnos" type="data" format="mothur.accnos" label="accnos - Group Names from your history"/> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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57 <param argument="list" type="data" format="mothur.list" optional="true" label="OTU List"/> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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58 <param argument="shared" type="data" format="mothur.shared" optional="true" label="OTU List OTU Shared file"/> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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59 <param argument="constaxonomy" type="data" format="mothur.cons.taxonomy" optional="true" label="contaxonomy - consensus taxonomy" |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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60 help="The contaxonomy file is the taxonomy file outputted by classify.otu"/> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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61 <param argument="otucorr" type="data" format="mothur.otu.corr" optional="true" label="OTU correlation file" |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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62 help="otu correlation coefficients are output by the otu.association command"/> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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63 <param argument="corraxes" type="data" format="mothur.axes" optional="true" label="Correlation axes file" |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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64 help="correlation axes file is output by the corr.axes command"/> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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65 |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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66 <conditional name="labelsource"> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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67 <param name="source" type="select" label="Select a label from"> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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68 <option value="list"> OTU list file </option> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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69 <option value="shared"> OTU shared file </option> |
0
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 </param> |
2
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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71 <when value="list"> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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72 <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label" |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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73 help="select exactly one label. If none selected, the first label in your file will be used"> |
0
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 <options> |
2
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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75 <filter type="data_meta" ref="list" key="labels"/> |
0
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 </options> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 </param> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 </when> |
2
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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79 <when value="shared"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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80 <param argument="label" type="select" optional="true" multiple="false" label="label - OTU Label" |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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81 help="select exactly one label. If none selected, the first label in your file will be used"> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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82 <options> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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83 <filter type="data_meta" ref="shared" key="labels"/> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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84 </options> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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85 </param> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 </when> |
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87 </conditional> |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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88 <expand macro="param-savelog"/> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 </inputs> |
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90 <outputs> |
a1aea42f0f8e
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91 <expand macro="logfile-output"/> |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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92 <data name="list_out" format="mothur.list" from_work_dir="list*.pick.*" label="${tool.name} on ${on_string}: pick.list"> |
04a479ceb84a
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93 <filter> $list </filter> |
04a479ceb84a
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94 </data> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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95 <data name="shared_out" format="mothur.shared" from_work_dir="shared*.pick.*" label="${tool.name} on ${on_string}: pick.shared"> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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96 <filter> $shared </filter> |
04a479ceb84a
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97 </data> |
04a479ceb84a
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98 <data name="constaxonomy_out" format="mothur.cons.taxonomy" from_work_dir="constaxonomy*.pick.*" label="${tool.name} on ${on_string}: pick.cons.taxonomy"> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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99 <filter> $constaxonomy </filter> |
04a479ceb84a
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100 </data> |
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101 <data name="otucorr_out" format="mothur.otu.corr" from_work_dir="otucorr*.pick.*" label="${tool.name} on ${on_string}: pick.otu.corr"> |
04a479ceb84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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102 <filter> $otucorr </filter> |
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103 </data> |
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104 <data name="corraxes_out" format="mothur.axes" from_work_dir="corraxes*.pick.*" label="${tool.name} on ${on_string}: pick.axes"> |
04a479ceb84a
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105 <filter> $corraxes </filter> |
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106 </data> |
0
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107 </outputs> |
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108 <tests> |
2
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109 <test><!-- test with list file input and default settings --> |
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110 <param name="list" value="amazon.an.list" ftype="mothur.list"/> |
04a479ceb84a
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111 <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/> |
04a479ceb84a
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112 <output name="list_out" ftype="mothur.list"> |
04a479ceb84a
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113 <assert_contents> |
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114 <expand macro="test-list-format"/> |
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115 <has_text text="unique"/> |
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116 <has_text text="Otu01"/> |
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117 <has_text text="Otu17"/> |
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118 <has_text text="Otu42"/> |
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119 <not_has_text text="Otu43"/> |
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120 </assert_contents> |
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121 </output> |
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122 <param name="savelog" value="true"/> |
0
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123 <expand macro="logfile-test"/> |
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124 </test> |
2
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125 <test><!-- test with shared and otu.corr file and label select --> |
04a479ceb84a
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126 <param name="shared" value="amazon.an.shared" ftype="mothur.shared"/> |
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127 <param name="accnos" value="amazon.otus.accnos" ftype="mothur.accnos"/> |
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128 <param name="label" value="0.03"/> |
2
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129 <param name="source" value="shared"/> |
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130 <param name="otucorr" value="amazon.an.0.03.pearson.otu.corr" ftype="mothur.cons.taxonomy"/> |
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131 <output name="shared_out" ftype="mothur.shared"> |
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132 <assert_contents> |
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133 <expand macro="test-shared-format"/> |
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134 <has_text text="0.03"/> |
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135 <has_text text="Otu01"/> |
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136 <has_text text="Otu17"/> |
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137 <has_text text="Otu42"/> |
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138 <not_has_text text="Otu43"/> |
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139 </assert_contents> |
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140 </output> |
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141 <param name="savelog" value="true"/> |
0
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142 <expand macro="logfile-test"/> |
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143 </test> |
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144 </tests> |
2
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145 <help><![CDATA[ |
0
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146 |
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147 @MOTHUR_OVERVIEW@ |
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148 |
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149 **Command Documentation** |
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150 |
2
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151 The get.otus command selects otus from a given list. |
0
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152 |
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153 .. _list: https://www.mothur.org/wiki/List_file |
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154 .. _get.otus: https://www.mothur.org/wiki/Get.otus |
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155 |
2
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156 ]]></help> |
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a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
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157 <expand macro="citations"/> |
a1aea42f0f8e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff
changeset
|
158 </tool> |