Mercurial > repos > iuc > mothur_otu_hierarchy

comparison otu.hierarchy.xml @ 0:7a4200446cbf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 06:00:15 -0400
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1 <tool profile="16.07" id="mothur_otu_hierarchy" name="Otu.hierarchy" version="@WRAPPER_VERSION@.0">
2 <description>Relate OTUs at different distances</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat &&
14
15 echo 'otu.hierarchy(
16 list=otu.dat,
17 label=$label1-$label2,
18 output=$output
19 )'
20 | sed 's/ //g' ## mothur trips over whitespace
21 | mothur
22 | tee mothur.out.log
23 ]]></command>
24 <inputs>
25 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
26 <param name="label1" type="select" label="label - OTU Label 1">
27 <expand macro="labeloptions"/>
28 </param>
29 <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1">
30 <expand macro="labeloptions"/>
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">
33 <option value="name" selected="true">OTU sequence names</option>
34 <option value="number">OTU numbers</option>
35 </param>
36 </inputs>
37 <outputs>
38 <expand macro="logfile-output"/>
39 <data name="hierarchy" format="tabular" from_work_dir="otu*.hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/>
40 </outputs>
41 <tests>
42 <test>
43 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
44 <param name="label1" value="0.05"/>
45 <param name="label2" value="0.03"/>
46 <output name="hierarchy" file="amazon.an.0.03.-.0.05.otu.hierarchy" ftype="tabular"/>
47 <expand macro="logfile-test"/>
48 </test>
49 </tests>
50 <help>
51 <![CDATA[
52
53 @MOTHUR_OVERVIEW@
54
55 **Command Documentation**
56
57 The otu.hierarchy_ command relates OTUs from a list_ at different distances.
58
59 .. _list: https://www.mothur.org/wiki/List_file
60 .. _otu.hierarchy: https://www.mothur.org/wiki/Otu.hierarchy
61
62 ]]>
63 </help>
64 <expand macro="citations"/>
65 </tool>