Mercurial > repos > iuc > mothur_deunique_tree

annotate deunique.tree.xml @ 3:6f140b20e011 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 22:10:19 -0400
parents 44d01ad18366
children 283af2e6130c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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90796e3ff3ef 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_deunique_tree" name="Deunique.tree" version="@WRAPPER_VERSION@.0">
90796e3ff3ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Reinsert the redundant sequence identiers back into a unique tree.</description>
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3 <macros>
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4 <import>macros.xml</import>
90796e3ff3ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
90796e3ff3ef 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"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
6f140b20e011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$tree' tree.dat &&
6f140b20e011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$names' names.dat &&
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16 echo 'deunique.tree(
6f140b20e011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 tree=tree.dat,
6f140b20e011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 name=names.dat
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19 )'
6f140b20e011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 | sed 's/ //g' ## mothur trips over whitespace
6f140b20e011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 | mothur
6f140b20e011 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 | tee mothur.out.log
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23 ]]></command>
90796e3ff3ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 <inputs>
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25 <param name="tree" type="data" format="mothur.tre" label="tree - Sequences to filter"/>
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26 <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/>
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27 <expand macro="param-savelog"/>
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28 </inputs>
90796e3ff3ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 <outputs>
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30 <expand macro="logfile-output"/>
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31 <data name="out_tree" format_source="tree" from_work_dir="tree*.deunique.tre" label="${tool.name} on ${on_string}: deunique.tre"/>
90796e3ff3ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="tree" value="treetest.tre"/>
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36 <param name="names" value="treetest.names"/>
90796e3ff3ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <output name="out_tree" file="treetest.deunique.tre"/>
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38 <param name="savelog" value="true"/>
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39 <expand macro="logfile-test"/>
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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44 @MOTHUR_OVERVIEW@
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47 **Command Documentation**
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49 The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file.
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51 .. _name: https://www.mothur.org/wiki/Name_file
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52 .. _deunique.tree: https://www.mothur.org/wiki/Deunique.tree
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54 v1.21.0: Updated to Mothur 1.33
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55
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56 ]]></help>
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57 <expand macro="citations"/>
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58 </tool>