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comparison pca.xml @ 3:194d0547e04d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 10:02:00 -0500
parents 258d04c1c5f8
children 6fe319c79f31
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2:a5e02397196f 3:194d0547e04d
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 'pca( 15 echo 'pca(
16 #if $otu.is_of_type("mothur.relabund"): 16 #if $otu.is_of_type("mothur.relabund"):
17 relabund=otu.dat, 17 relabund=otu.dat,
18 #elif $otu.is_of_type("mothur.shared"): 18 #elif $otu.is_of_type("mothur.shared"):
19 shared=otu.dat, 19 shared=otu.dat,
20 #end if 20 #end if
21 #if $label: 21 #if $label:
22 label=${ str($label).replace(",","-") }, 22 label=${ str($label).replace(",","-") },
23 #end if 23 #end if
24 #if $groups: 24 #if $groups:
25 groups=${ str($groups).replace(",","-") }, 25 groups=${ str($groups).replace(",","-") },
26 #end if 26 #end if
27 metric=$metric 27 metric=$metric
28 )' 28 )'
29 | sed 's/ //g' ## mothur trips over whitespace 29 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur 30 | mothur
31 | tee mothur.out.log 31 | tee mothur.out.log
32 ]]></command> 32 ]]></command>
33 <inputs> 33 <inputs>
34 <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"/>
35 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 35 <param name="label" type="select" label="label - OTU Labels" multiple="true">
36 <expand macro="labeloptions"/> 36 <expand macro="labeloptions"/>
63 <element name="0.55" md5="8c76b60484ffcab2ef7230e29071dd51" ftype="txt"/> 63 <element name="0.55" md5="8c76b60484ffcab2ef7230e29071dd51" ftype="txt"/>
64 </output_collection> 64 </output_collection>
65 <expand macro="logfile-test"/> 65 <expand macro="logfile-test"/>
66 </test> 66 </test>
67 </tests> 67 </tests>
68 <help> 68 <help><![CDATA[
69 <![CDATA[
70 69
71 @MOTHUR_OVERVIEW@ 70 @MOTHUR_OVERVIEW@
72 71
73 **Command Documentation** 72 **Command Documentation**
74 73
75 The pca_ command generate principle components plot data for a shared_ or relabund_ file. 74 The pca_ command generate principle components plot data for a shared_ or relabund_ file.
76 75
77 .. _shared: https://www.mothur.org/wiki/Shared_file 76 .. _shared: https://www.mothur.org/wiki/Shared_file
78 .. _relabund: https://www.mothur.org/wiki/Get.relabund 77 .. _relabund: https://www.mothur.org/wiki/Get.relabund
79 .. _pca: https://www.mothur.org/wiki/Pca 78 .. _pca: https://www.mothur.org/wiki/Pca
80 ]]> 79
81 </help> 80 ]]></help>
82 <expand macro="citations"/> 81 <expand macro="citations"/>
83 </tool> 82 </tool>