Mercurial > repos > iuc > mothur_cluster_classic

comparison cluster.classic.xml @ 1:f8dbdd8fb4bf 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 04:25:13 -0400
parents 1b88f1cd6f5f
children 6af6b54bed72
comparison
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0:1b88f1cd6f5f 1:f8dbdd8fb4bf
2 <description>Assign sequences to OTUs (Dotur implementation)</description> 2 <description>Assign sequences to OTUs (Dotur implementation)</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 "$dist" dist.dat && 13 ln -s "$dist" dist.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 16
27 precision=$precision, 30 precision=$precision,
28 sim=$sim 31 sim=$sim
29 )' 32 )'
30 | sed 's/ //g' ## mothur trips over whitespace 33 | sed 's/ //g' ## mothur trips over whitespace
31 | mothur 34 | mothur
35 | tee mothur.out.log
32 ]]></command> 36 ]]></command>
33 <inputs> 37 <inputs>
34 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/> 38 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/>
35 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 39 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
36 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 40 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
37 <param name="method" type="select" label="method - Select a Clustering Method" help=""> 41 <param name="method" type="select" label="method - Select a Clustering Method" help="">
38 <option value="furthest">Furthest neighbor</option> 42 <option value="furthest">Furthest neighbor</option>
39 <option value="nearest">Nearest neighbor</option> 43 <option value="nearest">Nearest neighbor</option>
76 <help> 80 <help>
77 <![CDATA[ 81 <![CDATA[
78 82
79 @MOTHUR_OVERVIEW@ 83 @MOTHUR_OVERVIEW@
80 84
81 **Command Documenation** 85 **Command Documentation**
82 86
83 The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit). 87 The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit).
84 88
85 .. _cluster.classic: http://www.mothur.org/wiki/Cluster.classic 89 .. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic
86 90
87 ]]> 91 ]]>
88 </help> 92 </help>
89 <expand macro="citations"/> 93 <expand macro="citations"/>
90 </tool> 94 </tool>