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comparison deunique.tree.xml @ 0:049d12e3c803 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:29:40 -0400
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-1:000000000000 0:049d12e3c803
1 <tool profile="16.07" id="mothur_deunique_tree" name="Deunique.tree" version="@WRAPPER_VERSION@.0">
2 <description>Reinsert the redundant sequence identiers back into a unique tree.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$tree" tree.dat &&
11 ln -s "$names" names.dat &&
12
13 echo 'deunique.tree(
14 tree=tree.dat,
15 name=names.dat
16 )'
17 | sed 's/ //g' ## mothur trips over whitespace
18 | mothur
19 ]]></command>
20 <inputs>
21 <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"/>
23 </inputs>
24 <outputs>
25 <expand macro="logfile-output"/>
26 <data name="out_tree" format_source="tree" from_work_dir="tree*.deunique.tre" label="${tool.name} on ${on_string}: deunique.tre"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="tree" value="treetest.tre"/>
31 <param name="names" value="treetest.names"/>
32 <output name="out_tree" file="treetest.deunique.tre"/>
33 <expand macro="logfile-test"/>
34 </test>
35 </tests>
36 <help>
37 <![CDATA[
38
39 @MOTHUR_OVERVIEW@
40
41
42 **Command Documenation**
43
44 The deunique.tree_ command is the reinserts the redundant sequence identiers back into a unique tree using a name_ file.
45
46 .. _name: http://www.mothur.org/wiki/Name_file
47 .. _deunique.tree: http://www.mothur.org/wiki/Deunique.tree
48
49 v1.21.0: Updated to Mothur 1.33
50
51 ]]>
52 </help>
53 <expand macro="citations"/>
54 </tool>