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comparison cluster.xml @ 1:c212b5d35bfe 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 05:08:26 -0400
parents 5d1b3989db21
children d7782c32375c
comparison
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0:5d1b3989db21 1:c212b5d35bfe
2 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> 2 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</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 "$matrix.dist" matrix.dist.dat && 13 ln -s "$matrix.dist" matrix.dist.dat &&
11 ln -s "$matrix.name" matrix.name.dat && 14 ln -s "$matrix.name" matrix.name.dat &&
12 ln -s "$count" count.dat && 15 ln -s "$count" count.dat &&
13 16
31 sim=$sim, 34 sim=$sim,
32 method=$method 35 method=$method
33 )' 36 )'
34 | sed 's/ //g' ## mothur trips over whitespace 37 | sed 's/ //g' ## mothur trips over whitespace
35 | mothur 38 | mothur
39 | tee mothur.out.log
36 ]]></command> 40 ]]></command>
37 <inputs> 41 <inputs>
38 <conditional name="matrix"> 42 <conditional name="matrix">
39 <param name="format" type="select" label="Select a Distance Matrix Format" help=""> 43 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
40 <option value="column">Pairwise Column Matrix</option> 44 <option value="column">Pairwise Column Matrix</option>
41 <option value="phylip">Phylip Distance Matrix</option> 45 <option value="phylip">Phylip Distance Matrix</option>
42 </param> 46 </param>
43 <when value="column"> 47 <when value="column">
44 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> 48 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
45 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> 49 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
46 </when> 50 </when>
47 <when value="phylip"> 51 <when value="phylip">
48 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 52 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
49 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 53 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
50 </when> 54 </when>
51 </conditional> 55 </conditional>
52 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 56 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
53 <param name="method" type="select" label="method - Select a Clustering Method" help=""> 57 <param name="method" type="select" label="method - Select a Clustering Method" help="">
96 <help> 100 <help>
97 <![CDATA[ 101 <![CDATA[
98 102
99 @MOTHUR_OVERVIEW@ 103 @MOTHUR_OVERVIEW@
100 104
101 **Command Documenation** 105 **Command Documentation**
102 106
103 The cluster_ command assign sequences to OTUs (Operational Taxonomy Unit). The assignment is based on a phylip-formatted_distance_matrix_ or a column-formatted_distance_matrix_ and name_ file. It generates a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file. 107 The cluster_ command assign sequences to OTUs (Operational Taxonomy Unit). The assignment is based on a phylip-formatted_distance_matrix_ or a column-formatted_distance_matrix_ and name_ file. It generates a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
104 108
105 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix 109 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
106 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix 110 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
107 .. _name: http://www.mothur.org/wiki/Name_file 111 .. _name: https://www.mothur.org/wiki/Name_file
108 .. _list: http://www.mothur.org/wiki/List_file 112 .. _list: https://www.mothur.org/wiki/List_file
109 .. _rabund: http://www.mothur.org/wiki/Rabund_file 113 .. _rabund: https://www.mothur.org/wiki/Rabund_file
110 .. _sabund: http://www.mothur.org/wiki/Sabund_file 114 .. _sabund: https://www.mothur.org/wiki/Sabund_file
111 .. _cluster: http://www.mothur.org/wiki/Cluster 115 .. _cluster: https://www.mothur.org/wiki/Cluster
112 116
113 ]]> 117 ]]>
114 </help> 118 </help>
115 <expand macro="citations"/> 119 <expand macro="citations"/>
116 </tool> 120 </tool>