Mercurial > repos > iuc > mothur_deunique_tree

comparison deunique.tree.xml @ 1:aad21e59489e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:51:27 -0400
parents 049d12e3c803
children 3ee6e1eab975
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0:049d12e3c803 1:aad21e59489e
2 <description>Reinsert the redundant sequence identiers back into a unique tree.</description> 2 <description>Reinsert the redundant sequence identiers back into a unique tree.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$tree" tree.dat && 13 ln -s "$tree" tree.dat &&
11 ln -s "$names" names.dat && 14 ln -s "$names" names.dat &&
12 15
13 echo 'deunique.tree( 16 echo 'deunique.tree(
14 tree=tree.dat, 17 tree=tree.dat,
15 name=names.dat 18 name=names.dat
16 )' 19 )'
17 | sed 's/ //g' ## mothur trips over whitespace 20 | sed 's/ //g' ## mothur trips over whitespace
18 | mothur 21 | mothur
22 | tee mothur.out.log
19 ]]></command> 23 ]]></command>
20 <inputs> 24 <inputs>
21 <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/> 25 <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/>
22 <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/> 26 <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/>
23 </inputs> 27 </inputs>
37 <![CDATA[ 41 <![CDATA[
38 42
39 @MOTHUR_OVERVIEW@ 43 @MOTHUR_OVERVIEW@
40 44
41 45
42 **Command Documenation** 46 **Command Documentation**
43 47
44 The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file. 48 The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file.
45 49
46 .. _name: http://www.mothur.org/wiki/Name_file 50 .. _name: https://www.mothur.org/wiki/Name_file
47 .. _deunique.tree: http://www.mothur.org/wiki/Deunique.tree 51 .. _deunique.tree: https://www.mothur.org/wiki/Deunique.tree
48 52
49 v1.21.0: Updated to Mothur 1.33 53 v1.21.0: Updated to Mothur 1.33
50 54
51 ]]> 55 ]]>
52 </help> 56 </help>