Mercurial > repos > iuc > mothur_cluster_classic

comparison cluster.classic.xml @ 0:872cb4f6fa0b 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 05:04:17 -0400
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children 085625ddf82c
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-1:000000000000 0:872cb4f6fa0b
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$dist" dist.dat &&
14 ln -s "$name" name.dat &&
15 ln -s "$count" count.dat &&
16
17 echo 'cluster.classic(
18 phylip=dist.dat,
19 #if $name:
20 name=name.dat,
21 #end if
22 #if $count:
23 count=count.dat,
24 #end if
25 method=$method,
26 #if $cutoff:
27 cutoff=$cutoff,
28 #end if
29 hard=$hard,
30 precision=$precision,
31 sim=$sim
32 )'
33 | sed 's/ //g' ## mothur trips over whitespace
34 | mothur
35 | tee mothur.out.log
36 ]]></command>
37 <inputs>
38 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/>
39 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
40 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
41 <param name="method" type="select" label="method - Select a Clustering Method" help="">
42 <option value="furthest">Furthest neighbor</option>
43 <option value="nearest">Nearest neighbor</option>
44 <option value="average" selected="true">Average neighbor</option>
45 <option value="weighted">Weighted</option>
46 </param>
47 <param name="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
48 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
49 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
50 <option value="10">.1</option>
51 <option value="100" selected="true">.01</option>
52 <option value="1000">.001</option>
53 <option value="10000">.0001</option>
54 <option value="100000">.00001</option>
55 <option value="1000000">.000001</option>
56 </param>
57 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
58 </inputs>
59 <outputs>
60 <expand macro="logfile-output"/>
61 <data name="rabund" format="mothur.rabund" from_work_dir="dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
62 <data name="sabund" format="mothur.sabund" from_work_dir="dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
63 <data name="otulist" format="mothur.list" from_work_dir="dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
64 </outputs>
65 <tests>
66 <test><!-- test with phylip and default params-->
67 <param name="dist" value="env.dist"/>
68 <output name="rabund" md5="b7f4b5ee46b2c4f5221d487e24dca9db" ftype="mothur.rabund"/>
69 <output name="sabund" md5="ac2df77e39a106fa65fae3d2132bc4ea" ftype="mothur.sabund"/>
70 <output name="otulist" ftype="mothur.list">
71 <assert_contents>
72 <has_text text="group"/>
73 <has_text text="unique"/>
74 <has_line_matching expression="^label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24$"/>
75 </assert_contents>
76 </output>
77 <expand macro="logfile-test"/>
78 </test>
79 </tests>
80 <help>
81 <![CDATA[
82
83 @MOTHUR_OVERVIEW@
84
85 **Command Documentation**
86
87 The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit).
88
89 .. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic
90
91 ]]>
92 </help>
93 <expand macro="citations"/>
94 </tool>