Mercurial > repos > iuc > mothur_otu_hierarchy

comparison otu.hierarchy.xml @ 2:058e6e36f6e5 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 22:20:51 -0400
parents 7a4200446cbf
children 2e82b56377d8
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1:844b22e17a4a 2:058e6e36f6e5
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 14
15 echo 'otu.hierarchy( 15 echo 'otu.hierarchy(
16 list=otu.dat, 16 list=otu.dat,
17 label=$label1-$label2, 17 label=$label1-$label2,
18 output=$output 18 output=$output
19 )' 19 )'
20 | sed 's/ //g' ## mothur trips over whitespace 20 | sed 's/ //g' ## mothur trips over whitespace
21 | mothur 21 | mothur
22 | tee mothur.out.log 22 | tee mothur.out.log
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 25 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
26 <param name="label1" type="select" label="label - OTU Label 1"> 26 <param name="label1" type="select" label="label - OTU Label 1">
27 <expand macro="labeloptions"/> 27 <expand macro="labeloptions"/>
31 </param> 31 </param>
32 <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers"> 32 <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers">
33 <option value="name" selected="true">OTU sequence names</option> 33 <option value="name" selected="true">OTU sequence names</option>
34 <option value="number">OTU numbers</option> 34 <option value="number">OTU numbers</option>
35 </param> 35 </param>
36 <expand macro="param-savelog"/>
36 </inputs> 37 </inputs>
37 <outputs> 38 <outputs>
38 <expand macro="logfile-output"/> 39 <expand macro="logfile-output"/>
39 <data name="hierarchy" format="tabular" from_work_dir="otu*.hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/> 40 <data name="hierarchy" format="tabular" from_work_dir="otu*.hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/>
40 </outputs> 41 </outputs>
42 <test> 43 <test>
43 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 44 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
44 <param name="label1" value="0.05"/> 45 <param name="label1" value="0.05"/>
45 <param name="label2" value="0.03"/> 46 <param name="label2" value="0.03"/>
46 <output name="hierarchy" file="amazon.an.0.03.-.0.05.otu.hierarchy" ftype="tabular"/> 47 <output name="hierarchy" file="amazon.an.0.03.-.0.05.otu.hierarchy" ftype="tabular"/>
48 <param name="savelog" value="true"/>
47 <expand macro="logfile-test"/> 49 <expand macro="logfile-test"/>
48 </test> 50 </test>
49 </tests> 51 </tests>
50 <help> 52 <help><![CDATA[
51 <![CDATA[
52 53
53 @MOTHUR_OVERVIEW@ 54 @MOTHUR_OVERVIEW@
54 55
55 **Command Documentation** 56 **Command Documentation**
56 57
57 The otu.hierarchy_ command relates OTUs from a list_ at different distances. 58 The otu.hierarchy_ command relates OTUs from a list_ at different distances.
58 59
59 .. _list: https://www.mothur.org/wiki/List_file 60 .. _list: https://www.mothur.org/wiki/List_file
60 .. _otu.hierarchy: https://www.mothur.org/wiki/Otu.hierarchy 61 .. _otu.hierarchy: https://www.mothur.org/wiki/Otu.hierarchy
61 62
62 ]]> 63 ]]></help>
63 </help>
64 <expand macro="citations"/> 64 <expand macro="citations"/>
65 </tool> 65 </tool>