Mercurial > repos > iuc > mothur_cluster
comparison cluster.xml @ 0:8c1b609f566d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 05:40:08 -0400 |
parents | |
children | 6f2cdccbfa48 |
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-1:000000000000 | 0:8c1b609f566d |
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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="stdio"/> | |
8 <expand macro="version_command"/> | |
9 <command><![CDATA[ | |
10 @SHELL_OPTIONS@ | |
11 | |
12 ## create symlinks to input datasets | |
13 ln -s "$matrix.dist" matrix.dist.dat && | |
14 ln -s "$matrix.name" matrix.name.dat && | |
15 ln -s "$count" count.dat && | |
16 | |
17 echo 'cluster( | |
18 #if $matrix.format == "phylip": | |
19 phylip=matrix.dist.dat, | |
20 #else | |
21 column=matrix.dist.dat, | |
22 #end if | |
23 #if $matrix.name: | |
24 name=matrix.name.dat, | |
25 #end if | |
26 #if $count: | |
27 count=count.dat, | |
28 #end if | |
29 hard=$hard, | |
30 #if float($cutoff) > 0.0: | |
31 cutoff=$cutoff, | |
32 #end if | |
33 precision=$precision, | |
34 sim=$sim, | |
35 method=$method | |
36 )' | |
37 | sed 's/ //g' ## mothur trips over whitespace | |
38 | mothur | |
39 | tee mothur.out.log | |
40 ]]></command> | |
41 <inputs> | |
42 <conditional name="matrix"> | |
43 <param name="format" type="select" label="Select a Distance Matrix Format" help=""> | |
44 <option value="column">Pairwise Column Matrix</option> | |
45 <option value="phylip">Phylip Distance Matrix</option> | |
46 </param> | |
47 <when value="column"> | |
48 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> | |
49 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> | |
50 </when> | |
51 <when value="phylip"> | |
52 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> | |
53 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> | |
54 </when> | |
55 </conditional> | |
56 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> | |
57 <param name="method" type="select" label="method - Select a Clustering Method" help=""> | |
58 <option value="furthest">Furthest neighbor</option> | |
59 <option value="nearest">Nearest neighbor</option> | |
60 <option value="average" selected="true">Average neighbor</option> | |
61 <option value="weighted">Weighted</option> | |
62 </param> | |
63 <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"/> | |
64 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/> | |
65 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths"> | |
66 <option value="10">.1</option> | |
67 <option value="100" selected="true">.01</option> | |
68 <option value="1000">.001</option> | |
69 <option value="10000">.0001</option> | |
70 <option value="100000">.00001</option> | |
71 <option value="1000000">.000001</option> | |
72 </param> | |
73 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/> | |
74 </inputs> | |
75 <outputs> | |
76 <expand macro="logfile-output"/> | |
77 <data name="rabund" format="mothur.rabund" from_work_dir="matrix.dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> | |
78 <data name="sabund" format="mothur.sabund" from_work_dir="matrix.dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> | |
79 <data name="otulist" format="mothur.list" from_work_dir="matrix.dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/> | |
80 </outputs> | |
81 <tests> | |
82 <test><!-- test with phylip input --> | |
83 <param name="format" value="phylip"/> | |
84 <param name="dist" value="amazon.dist"/> | |
85 <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/> | |
86 <output name="sabund" file="amazon.an.sabund" ftype="mothur.sabund"/> | |
87 <output name="otulist" md5="a6bf2a6ef7950b3ee2aa5bff4a662b6d" ftype="mothur.list"/> | |
88 <expand macro="logfile-test"/> | |
89 </test> | |
90 <test><!-- test with column input --> | |
91 <param name="format" value="column"/> | |
92 <param name="dist" value="amazon.pair.dist"/> | |
93 <param name="name" value="amazon.names"/> | |
94 <output name="rabund" md5="ec88216404729d0f4a0463e50e60c9ad" ftype="mothur.rabund"/> | |
95 <output name="sabund" md5="f2c714531430b98d8cdfd3497468eec2" ftype="mothur.sabund"/> | |
96 <output name="otulist" md5="1769463ed0b6680babe5801bf9c0a85c" ftype="mothur.list"/> | |
97 <expand macro="logfile-test"/> | |
98 </test> | |
99 </tests> | |
100 <help> | |
101 <![CDATA[ | |
102 | |
103 @MOTHUR_OVERVIEW@ | |
104 | |
105 **Command Documentation** | |
106 | |
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. | |
108 | |
109 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix | |
110 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix | |
111 .. _name: https://www.mothur.org/wiki/Name_file | |
112 .. _list: https://www.mothur.org/wiki/List_file | |
113 .. _rabund: https://www.mothur.org/wiki/Rabund_file | |
114 .. _sabund: https://www.mothur.org/wiki/Sabund_file | |
115 .. _cluster: https://www.mothur.org/wiki/Cluster | |
116 | |
117 ]]> | |
118 </help> | |
119 <expand macro="citations"/> | |
120 </tool> |