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comparison pca.xml @ 1:258d04c1c5f8 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 04:55:35 -0400
parents 52a9971dc4fa
children 194d0547e04d
comparison
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0:52a9971dc4fa 1:258d04c1c5f8
2 <description>Principal Coordinate Analysis for a shared file</description> 2 <description>Principal Coordinate Analysis for a shared file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
11 14
12 echo 'pca( 15 echo 'pca(
13 #if $otu.is_of_type("mothur.relabund"): 16 #if $otu.is_of_type("mothur.relabund"):
23 #end if 26 #end if
24 metric=$metric 27 metric=$metric
25 )' 28 )'
26 | sed 's/ //g' ## mothur trips over whitespace 29 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur 30 | mothur
31 | tee mothur.out.log
28 ]]></command> 32 ]]></command>
29 <inputs> 33 <inputs>
30 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/> 34 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
31 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 35 <param name="label" type="select" label="label - OTU Labels" multiple="true">
32 <expand macro="labeloptions"/> 36 <expand macro="labeloptions"/>
64 <help> 68 <help>
65 <![CDATA[ 69 <![CDATA[
66 70
67 @MOTHUR_OVERVIEW@ 71 @MOTHUR_OVERVIEW@
68 72
69 **Command Documenation** 73 **Command Documentation**
70 74
71 The pca_ command generate principle components plot data for a shared_ or relabund_ file. 75 The pca_ command generate principle components plot data for a shared_ or relabund_ file.
72 76
73 .. _shared: http://www.mothur.org/wiki/Shared_file 77 .. _shared: https://www.mothur.org/wiki/Shared_file
74 .. _relabund: http://www.mothur.org/wiki/Get.relabund 78 .. _relabund: https://www.mothur.org/wiki/Get.relabund
75 .. _pca: http://www.mothur.org/wiki/Pca 79 .. _pca: https://www.mothur.org/wiki/Pca
76 ]]> 80 ]]>
77 </help> 81 </help>
78 <expand macro="citations"/> 82 <expand macro="citations"/>
79 </tool> 83 </tool>