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comparison consensus.seqs.xml @ 1:fb0eb9393fa8 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 05:09:44 -0400
parents fb865c8dc76f
children 05195067dd2e
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0:fb865c8dc76f 1:fb0eb9393fa8
2 <description>Find a consensus sequence for each OTU or phylotype</description> 2 <description>Find a consensus sequence for each OTU or phylotype</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 "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 ln -s "$name" name.dat && 14 ln -s "$name" name.dat &&
12 ln -s "$count" count.dat && 15 ln -s "$count" count.dat &&
13 #if $perotu.use == "yes": 16 #if $perotu.use == "yes":
32 ,count=count.dat 35 ,count=count.dat
33 #end if 36 #end if
34 )' 37 )'
35 | sed 's/ //g' ## mothur trips over whitespace 38 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur 39 | mothur
40 | tee mothur.out.log
37 ]]></command> 41 ]]></command>
38 <inputs> 42 <inputs>
39 <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/> 43 <param name="fasta" type="data" format="mothur.align" label="fasta - Sequences to Bin" help="Sequences must be aligned"/>
40 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 44 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
41 <conditional name="perotu"> 45 <conditional name="perotu">
103 <help> 107 <help>
104 <![CDATA[ 108 <![CDATA[
105 109
106 @MOTHUR_OVERVIEW@ 110 @MOTHUR_OVERVIEW@
107 111
108 **Command Documenation** 112 **Command Documentation**
109 113
110 The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned. 114 The consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned.
111 115
112 .. _consensus.seqs: http://www.mothur.org/wiki/Consensus.seqs 116 .. _consensus.seqs: https://www.mothur.org/wiki/Consensus.seqs
113 ]]> 117 ]]>
114 </help> 118 </help>
115 <expand macro="citations"/> 119 <expand macro="citations"/>
116 </tool> 120 </tool>