Mercurial > repos > iuc > mothur_make_lefse

comparison make.lefse.xml @ 1:cb917d37d403 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 05:05:34 -0400
parents 2f6aaf8b5068
children e9cd4b205ddd
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0:2f6aaf8b5068 1:cb917d37d403
2 <description>create a lefse formatted input file from mothur's output files</description> 2 <description>create a lefse formatted input file from mothur's output files</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 ln -s "$design" design.dat && 14 ln -s "$design" design.dat &&
12 ln -s "$constaxonomy" constaxonomy.dat && 15 ln -s "$constaxonomy" constaxonomy.dat &&
13 16
28 #end if 31 #end if
29 scale=$scale 32 scale=$scale
30 )' 33 )'
31 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur 35 | mothur
36 | tee mothur.out.log
33 ]]></command> 37 ]]></command>
34 <inputs> 38 <inputs>
35 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/> 39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - provide a shared or relabund file"/>
36 <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used"> 40 <param name="label" type="select" optional="true" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
37 <expand macro="labeloptions"/> 41 <expand macro="labeloptions"/>
66 <help> 70 <help>
67 <![CDATA[ 71 <![CDATA[
68 72
69 @MOTHUR_OVERVIEW@ 73 @MOTHUR_OVERVIEW@
70 74
71 **Command Documenation** 75 **Command Documentation**
72 76
73 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files. 77 The make.lefse_ allows you to create a lefse formatted input file from mothur's output files.
74 78
75 .. _make.lefse: http://www.mothur.org/wiki/Make.lefse 79 .. _make.lefse: https://www.mothur.org/wiki/Make.lefse
76 80
77 ]]> 81 ]]>
78 </help> 82 </help>
79 <citations> 83 <citations>
80 <citation type="doi">10.1128/AEM.01541-09</citation> 84 <citation type="doi">10.1128/AEM.01541-09</citation>