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comparison pcoa.xml @ 0:57b46e1032ad 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 05:01:28 -0400
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-1:000000000000 0:57b46e1032ad
1 <tool profile="16.07" id="mothur_pcoa" name="Pcoa" version="@WRAPPER_VERSION@.0">
2 <description>Principal Coordinate Analysis for a distance matrix</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 "$phylip" phylip.dat &&
14
15 echo 'pcoa(
16 phylip=phylip.dat,
17 metric=$metric
18 )'
19 | sed 's/ //g' ## mothur trips over whitespace
20 | mothur
21 | tee mothur.out.log
22 ]]></command>
23 <inputs>
24 <param name="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/>
25 <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
26 </inputs>
27 <outputs>
28 <expand macro="logfile-output"/>
29 <data name="pcoa" format="mothur.axes" from_work_dir="phylip*.pcoa.axes" label="${tool.name} on ${on_string}: pcoa.axes"/>
30 <data name="loadings" format="tabular" from_work_dir="phylip*.pcoa.loadings" label="${tool.name} on ${on_string}: loadings"/>
31 </outputs>
32 <tests>
33 <test>
34 <param name="phylip" value="amazon.dist"/>
35 <output name="pcoa" file="amazon.pcoa.axes"/>
36 <output name="loadings" file="amazon.pcoa.loadings"/>
37 <expand macro="logfile-test"/>
38 </test>
39 </tests>
40 <help>
41 <![CDATA[
42
43 @MOTHUR_OVERVIEW@
44
45 **Command Documentation**
46
47 The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_.
48
49 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
50 .. _pcoa: https://www.mothur.org/wiki/Pcoa
51 ]]>
52 </help>
53 <expand macro="citations"/>
54 </tool>