Mercurial > repos > iuc > mothur_normalize_shared

comparison normalize.shared.xml @ 1:00df9f248874 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 18:14:50 -0400
parents ed349f5c32fe
children 6ce70e21be87
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0:ed349f5c32fe 1:00df9f248874
2 <description>Normalize the number of sequences per group to a specified level</description> 2 <description>Normalize the number of sequences per group to a specified level</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 'normalize.shared( 15 echo 'normalize.shared(
13 #if $otu.is_of_type("mothur.relabund"): 16 #if $otu.is_of_type("mothur.relabund"):
26 ,method=${ str($method).replace(",","-") } 29 ,method=${ str($method).replace(",","-") }
27 #end if 30 #end if
28 )' 31 )'
29 | sed 's/ //g' ## mothur trips over whitespace 32 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur 33 | mothur
34 | tee mothur.out.log
31 ]]></command> 35 ]]></command>
32 <inputs> 36 <inputs>
33 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/> 37 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
34 <param name="label" type="select" multiple="true" label="label - OTU Labels"> 38 <param name="label" type="select" multiple="true" label="label - OTU Labels">
35 <expand macro="labeloptions"/> 39 <expand macro="labeloptions"/>
73 <help> 77 <help>
74 <![CDATA[ 78 <![CDATA[
75 79
76 @MOTHUR_OVERVIEW@ 80 @MOTHUR_OVERVIEW@
77 81
78 **Command Documenation** 82 **Command Documentation**
79 83
80 The normalize.shared_ command normalizes the number of sequences per group to a specified level. The input is a shared_ or relabund_ file. 84 The normalize.shared_ command normalizes the number of sequences per group to a specified level. The input is a shared_ or relabund_ file.
81 85
82 .. _shared: http://www.mothur.org/wiki/Shared_file 86 .. _shared: https://www.mothur.org/wiki/Shared_file
83 .. _relabund: http://www.mothur.org/wiki/Get.relabund 87 .. _relabund: https://www.mothur.org/wiki/Get.relabund
84 .. _normalize.shared: http://www.mothur.org/wiki/Normalize.shared 88 .. _normalize.shared: https://www.mothur.org/wiki/Normalize.shared
85 ]]> 89 ]]>
86 </help> 90 </help>
87 <expand macro="citations"/> 91 <expand macro="citations"/>
88 </tool> 92 </tool>