Mercurial > repos > iuc > mothur_pcoa

comparison pcoa.xml @ 2:3c560e5c3dd2 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 22:18:05 -0400
parents 57b46e1032ad
children c9fc98593dec
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1:8a69122b082f 2:3c560e5c3dd2
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 "$phylip" phylip.dat && 13 ln -s '$phylip' phylip.dat &&
14 14
15 echo 'pcoa( 15 echo 'pcoa(
16 phylip=phylip.dat, 16 phylip=phylip.dat,
17 metric=$metric 17 metric=$metric
18 )' 18 )'
19 | sed 's/ //g' ## mothur trips over whitespace 19 | sed 's/ //g' ## mothur trips over whitespace
20 | mothur 20 | mothur
21 | tee mothur.out.log 21 | tee mothur.out.log
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <param name="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/> 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"/> 25 <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
26 <expand macro="param-savelog"/>
26 </inputs> 27 </inputs>
27 <outputs> 28 <outputs>
28 <expand macro="logfile-output"/> 29 <expand macro="logfile-output"/>
29 <data name="pcoa" format="mothur.axes" from_work_dir="phylip*.pcoa.axes" label="${tool.name} on ${on_string}: pcoa.axes"/> 30 <data name="pcoa" format="mothur.axes" from_work_dir="phylip*.pcoa.axes" label="${tool.name} on ${on_string}: pcoa.axes"/>
30 <data name="loadings" format="tabular" from_work_dir="phylip*.pcoa.loadings" label="${tool.name} on ${on_string}: loadings"/> 31 <data name="loadings" format="tabular" from_work_dir="phylip*.pcoa.loadings" label="${tool.name} on ${on_string}: loadings"/>
32 <tests> 33 <tests>
33 <test> 34 <test>
34 <param name="phylip" value="amazon.dist"/> 35 <param name="phylip" value="amazon.dist"/>
35 <output name="pcoa" file="amazon.pcoa.axes"/> 36 <output name="pcoa" file="amazon.pcoa.axes"/>
36 <output name="loadings" file="amazon.pcoa.loadings"/> 37 <output name="loadings" file="amazon.pcoa.loadings"/>
38 <param name="savelog" value="true"/>
37 <expand macro="logfile-test"/> 39 <expand macro="logfile-test"/>
38 </test> 40 </test>
39 </tests> 41 </tests>
40 <help> 42 <help><![CDATA[
41 <![CDATA[
42 43
43 @MOTHUR_OVERVIEW@ 44 @MOTHUR_OVERVIEW@
44 45
45 **Command Documentation** 46 **Command Documentation**
46 47
47 The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_. 48 The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_.
48 49
49 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix 50 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
50 .. _pcoa: https://www.mothur.org/wiki/Pcoa 51 .. _pcoa: https://www.mothur.org/wiki/Pcoa
51 ]]> 52
52 </help> 53 ]]></help>
53 <expand macro="citations"/> 54 <expand macro="citations"/>
54 </tool> 55 </tool>