Mercurial > repos > iuc > mothur_filter_shared
annotate filter.shared.xml @ 9:2d1dbf69f589 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author | iuc |
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date | Thu, 21 Jan 2021 23:46:00 +0000 |
parents | e44c38a17c7a |
children | c8c3b2271c87 |
rev | line source |
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0
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_filter_shared" name="Filter.shared" version="@WRAPPER_VERSION@.0"> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>remove OTUs based on various critieria</description> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros> |
bccb5efbc4ee
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> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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5 </macros> |
bccb5efbc4ee
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"/> |
bccb5efbc4ee
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"/> |
bccb5efbc4ee
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"/> |
bccb5efbc4ee
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
644b7baba854
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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bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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11 |
2
644b7baba854
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 |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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13 ln -s '$otu' otu.dat && |
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bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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14 |
2
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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15 echo 'filter.shared( |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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16 shared=otu.dat, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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17 #if $label: |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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18 label=${ str($label).replace(",","-") }, |
644b7baba854
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 |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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20 #if $label: |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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21 groups=${ str($groups).replace(",","-") }, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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22 #end if |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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23 minabund=$minabund, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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24 minpercent=$minpercent, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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25 rarepercent=$rarepercent, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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26 keepties=$keepties, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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27 minnumsamples=$minnumsamples, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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28 minpercentsamples=$minpercentsamples, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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29 mintotal=$mintotal, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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30 makerare=$makerare |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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31 )' |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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32 | sed 's/ //g' ## mothur trips over whitespace |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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33 | mothur |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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34 | tee mothur.out.log |
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bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 ]]></command> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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36 <inputs> |
2
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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37 <param name="otu" argument="shared" type="data" format="mothur.shared" label="shared - specify your shared file"/> |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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38 <param argument="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output"> |
0
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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39 <expand macro="labeloptions"/> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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40 </param> |
2
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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41 <param argument="groups" type="select" optional="true" multiple="true" label="Select groups for to include in this grouping"> |
0
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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42 <options> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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43 <filter type="data_meta" ref="otu" key="groups"/> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
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44 </options> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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45 </param> |
2
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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46 <param argument="minabund" type="integer" value="0" min="0" label="minabund - indicate the minimum abundance required for each sample in a given OTU" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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47 help="If any samples abundance falls below the minimum, the OTU is removed"/> |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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48 <param argument="minpercent" type="integer" value="0" min="0" max="100" label="minpercent - indicate the minimum relative abundance of an OTU" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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49 help="For example, if the OTUs total abundance across all samples is 8, and the total abundance across all OTUs is 1000, and minpercent=1. |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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50 The OTU's relative abundance is 0.008, the minimum is 0.01, so the OTU will be removed"/> |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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51 <param argument="rarepercent" type="integer" value="0" min="0" max="100" label="rarepercent - indicate the percentage of otus to remove" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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52 help="The OTUs chosen to be removed are the rarest. For example if you have 1000 OTUs, rarepercent=20 would remove the 200 OTUs with the lowest abundance"/> |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents:
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53 <param argument="keepties" type="boolean" truevalue="true" falsevalue="false" checked="true" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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54 label="keepties - indicate you want to keep the OTUs with the same abundance as the first 'not rare' OTU" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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55 help="For example if you have 10 OTUs, rarepercent=20 abundances of 20, 18, 15, 15, 10, 5, 3, 3, 3, 1. keepties=t, would remove the 10th OTU, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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56 but keep the 9th because its abundance ties the 8th OTU. keepties=f would remove OTUs 9 and 10"/> |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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57 <param argument="minnumsamples" type="integer" value="0" min="0" label="minnumsamples - indicate the minimum number of samples present in an OTU" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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58 help="If the number of samples present falls below the minimum, the OTU is removed"/> |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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59 <param argument="minpercentsamples" type="integer" value="0" min="0" max="100" label="minpercentsamples - indicate the minimum percent of sample present in an OTU" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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60 help="For example, if the total number of samples is 10, the number present is 3, and the minpercentsamples=50. The OTU's precent of samples is 0.333, |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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61 the minimum is 0.50, so the OTU will be removed (Default=0)"/> |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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62 <param argument="mintotal" type="integer" value="0" min="0" max="100" label="mintotal - indicate the minimum abundance required for a given OTU" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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63 help="If abundance across all samples falls below the minimum, the OTU is removed"/> |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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64 <param argument="makerare" type="boolean" truevalue="true" falsevalue="false" checked="true" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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65 label="makerare - indicate you want the abundances of any removed OTUs to be saved and a new rare OTU created with its abundances equal to the sum of the OTUs removed" |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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66 help="This will preserve the number of reads in your dataset"/> |
644b7baba854
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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67 <expand macro="param-savelog"/> |
0
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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68 </inputs> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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69 <outputs> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 <expand macro="logfile-output"/> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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71 <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared"> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 <discover_datasets pattern=".*?\.(?P<designation>.*)\.filter\.dat" format="mothur.shared"/> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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73 </collection> |
bccb5efbc4ee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 </outputs> |
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75 <tests> |
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76 <test><!-- test with defaults --> |
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77 <param name="otu" value="esophagus.fn.shared" ftype="mothur.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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78 <output_collection name="filter_shared" count="4"> |
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79 <element name="0.03" ftype="mothur.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 <assert_contents> |
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81 <expand macro="test-shared-format"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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82 <has_text text="0.03"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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83 </assert_contents> |
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84 </element> |
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85 </output_collection> |
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86 <param name="savelog" value="true"/> |
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87 <expand macro="logfile-test"/> |
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88 </test> |
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89 <test><!-- test with label and group select --> |
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90 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
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91 <param name="label" value="0.05,0.29,0.33"/> |
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92 <param name="groups" value="forest,pasture"/> |
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93 <param name="minabund" value="1"/> |
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94 <output_collection name="filter_shared" count="3"> |
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95 <element name="0.29" ftype="mothur.shared"> |
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96 <assert_contents> |
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97 <expand macro="test-shared-format"/> |
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98 <has_text text="0.29"/> |
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99 </assert_contents> |
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100 </element> |
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101 </output_collection> |
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102 <param name="savelog" value="true"/> |
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103 <expand macro="logfile-test"/> |
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104 </test> |
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105 </tests> |
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106 <help><![CDATA[ |
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107 |
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108 @MOTHUR_OVERVIEW@ |
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109 |
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110 **Command Documentation** |
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111 |
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112 The filter.shared_ is used to remove OTUs based on various critieria. |
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113 |
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114 .. _filter.shared: https://www.mothur.org/wiki/Filter.shared |
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115 |
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116 ]]></help> |
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117 <expand macro="citations"/> |
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118 </tool> |