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comparison cluster.classic.xml @ 0:1b88f1cd6f5f 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 17:37:42 -0400
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-1:000000000000 0:1b88f1cd6f5f
1 <tool profile="16.07" id="mothur_cluster_classic" name="Cluster.classic" version="@WRAPPER_VERSION@.0">
2 <description>Assign sequences to OTUs (Dotur implementation)</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 "$dist" dist.dat &&
11 ln -s "$name" name.dat &&
12 ln -s "$count" count.dat &&
13
14 echo 'cluster.classic(
15 phylip=dist.dat,
16 #if $name:
17 name=name.dat,
18 #end if
19 #if $count:
20 count=count.dat,
21 #end if
22 method=$method,
23 #if $cutoff:
24 cutoff=$cutoff,
25 #end if
26 hard=$hard,
27 precision=$precision,
28 sim=$sim
29 )'
30 | sed 's/ //g' ## mothur trips over whitespace
31 | mothur
32 ]]></command>
33 <inputs>
34 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/>
35 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
36 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
37 <param name="method" type="select" label="method - Select a Clustering Method" help="">
38 <option value="furthest">Furthest neighbor</option>
39 <option value="nearest">Nearest neighbor</option>
40 <option value="average" selected="true">Average neighbor</option>
41 <option value="weighted">Weighted</option>
42 </param>
43 <param name="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
44 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
45 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
46 <option value="10">.1</option>
47 <option value="100" selected="true">.01</option>
48 <option value="1000">.001</option>
49 <option value="10000">.0001</option>
50 <option value="100000">.00001</option>
51 <option value="1000000">.000001</option>
52 </param>
53 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
54 </inputs>
55 <outputs>
56 <expand macro="logfile-output"/>
57 <data name="rabund" format="mothur.rabund" from_work_dir="dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
58 <data name="sabund" format="mothur.sabund" from_work_dir="dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
59 <data name="otulist" format="mothur.list" from_work_dir="dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
60 </outputs>
61 <tests>
62 <test><!-- test with phylip and default params-->
63 <param name="dist" value="env.dist"/>
64 <output name="rabund" md5="b7f4b5ee46b2c4f5221d487e24dca9db" ftype="mothur.rabund"/>
65 <output name="sabund" md5="ac2df77e39a106fa65fae3d2132bc4ea" ftype="mothur.sabund"/>
66 <output name="otulist" ftype="mothur.list">
67 <assert_contents>
68 <has_text text="group"/>
69 <has_text text="unique"/>
70 <has_line_matching expression="^label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24$"/>
71 </assert_contents>
72 </output>
73 <expand macro="logfile-test"/>
74 </test>
75 </tests>
76 <help>
77 <![CDATA[
78
79 @MOTHUR_OVERVIEW@
80
81 **Command Documenation**
82
83 The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit).
84
85 .. _cluster.classic: http://www.mothur.org/wiki/Cluster.classic
86
87 ]]>
88 </help>
89 <expand macro="citations"/>
90 </tool>