Mercurial > repos > iuc > mothur_get_label

comparison get.label.xml @ 1:83cf3f511e72 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:12:03 -0400
parents 8dd86660e447
children 6d082f402534
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0:8dd86660e447 1:83cf3f511e72
2 <description>label names from list, sabund, or rabund file</description> 2 <description>label names from list, sabund, or rabund 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 'get.label( 15 echo 'get.label(
13 #if $otu.is_of_type("mothur.rabund"): 16 #if $otu.is_of_type("mothur.rabund"):
17 #else 20 #else
18 list=otu.dat 21 list=otu.dat
19 #end if 22 #end if
20 )' 23 )'
21 | sed 's/ //g' ## mothur trips over whitespace 24 | sed 's/ //g' ## mothur trips over whitespace
22 | mothur && 25 | mothur
26 | tee mothur.out.log &&
23 27
24 ## parse relevant output from logfile to file 28 ## parse relevant output from logfile to file
25 cat mothur.*.logfile 29 cat mothur.*.logfile
26 | head -n-3 30 | head -n-3
27 | sed '1,29d' 31 | sed '1,29d'
54 <help> 58 <help>
55 <![CDATA[ 59 <![CDATA[
56 60
57 @MOTHUR_OVERVIEW@ 61 @MOTHUR_OVERVIEW@
58 62
59 **Command Documenation** 63 **Command Documentation**
60 64
61 The get.label_ command generate principle components plot data. 65 The get.label_ command generate principle components plot data.
62 66
63 .. _get.label: http://www.mothur.org/wiki/Get.label 67 .. _get.label: https://www.mothur.org/wiki/Get.label
64 68
65 v.1.20.0: Updated to Mothur 1.33 69 v.1.20.0: Updated to Mothur 1.33
66 ]]> 70 ]]>
67 </help> 71 </help>
68 <expand macro="citations"/> 72 <expand macro="citations"/>