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comparison cluster.xml @ 0:5d1b3989db21 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:26:41 -0400
parents
children c212b5d35bfe
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-1:000000000000 0:5d1b3989db21
1 <tool profile="16.07" id="mothur_cluster" name="Cluster" version="@WRAPPER_VERSION@.0">
2 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$matrix.dist" matrix.dist.dat &&
11 ln -s "$matrix.name" matrix.name.dat &&
12 ln -s "$count" count.dat &&
13
14 echo 'cluster(
15 #if $matrix.format == "phylip":
16 phylip=matrix.dist.dat,
17 #else
18 column=matrix.dist.dat,
19 #end if
20 #if $matrix.name:
21 name=matrix.name.dat,
22 #end if
23 #if $count:
24 count=count.dat,
25 #end if
26 hard=$hard,
27 #if float($cutoff) > 0.0:
28 cutoff=$cutoff,
29 #end if
30 precision=$precision,
31 sim=$sim,
32 method=$method
33 )'
34 | sed 's/ //g' ## mothur trips over whitespace
35 | mothur
36 ]]></command>
37 <inputs>
38 <conditional name="matrix">
39 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
40 <option value="column">Pairwise Column Matrix</option>
41 <option value="phylip">Phylip Distance Matrix</option>
42 </param>
43 <when value="column">
44 <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"/>
46 </when>
47 <when value="phylip">
48 <param name="dist" type="data" format="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"/>
50 </when>
51 </conditional>
52 <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="">
54 <option value="furthest">Furthest neighbor</option>
55 <option value="nearest">Nearest neighbor</option>
56 <option value="average" selected="true">Average neighbor</option>
57 <option value="weighted">Weighted</option>
58 </param>
59 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0.0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
60 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
61 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
62 <option value="10">.1</option>
63 <option value="100" selected="true">.01</option>
64 <option value="1000">.001</option>
65 <option value="10000">.0001</option>
66 <option value="100000">.00001</option>
67 <option value="1000000">.000001</option>
68 </param>
69 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
70 </inputs>
71 <outputs>
72 <expand macro="logfile-output"/>
73 <data name="rabund" format="mothur.rabund" from_work_dir="matrix.dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
74 <data name="sabund" format="mothur.sabund" from_work_dir="matrix.dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
75 <data name="otulist" format="mothur.list" from_work_dir="matrix.dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
76 </outputs>
77 <tests>
78 <test><!-- test with phylip input -->
79 <param name="format" value="phylip"/>
80 <param name="dist" value="amazon.dist"/>
81 <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/>
82 <output name="sabund" file="amazon.an.sabund" ftype="mothur.sabund"/>
83 <output name="otulist" md5="a6bf2a6ef7950b3ee2aa5bff4a662b6d" ftype="mothur.list"/>
84 <expand macro="logfile-test"/>
85 </test>
86 <test><!-- test with column input -->
87 <param name="format" value="column"/>
88 <param name="dist" value="amazon.pair.dist"/>
89 <param name="name" value="amazon.names"/>
90 <output name="rabund" md5="ec88216404729d0f4a0463e50e60c9ad" ftype="mothur.rabund"/>
91 <output name="sabund" md5="f2c714531430b98d8cdfd3497468eec2" ftype="mothur.sabund"/>
92 <output name="otulist" md5="1769463ed0b6680babe5801bf9c0a85c" ftype="mothur.list"/>
93 <expand macro="logfile-test"/>
94 </test>
95 </tests>
96 <help>
97 <![CDATA[
98
99 @MOTHUR_OVERVIEW@
100
101 **Command Documenation**
102
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.
104
105 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
106 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
107 .. _name: http://www.mothur.org/wiki/Name_file
108 .. _list: http://www.mothur.org/wiki/List_file
109 .. _rabund: http://www.mothur.org/wiki/Rabund_file
110 .. _sabund: http://www.mothur.org/wiki/Sabund_file
111 .. _cluster: http://www.mothur.org/wiki/Cluster
112
113 ]]>
114 </help>
115 <expand macro="citations"/>
116 </tool>