Mercurial > repos > iuc > mothur_cluster_classic

comparison cluster.classic.xml @ 2:085625ddf82c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:15:53 -0400
parents 872cb4f6fa0b
children 6ba59950d95c
comparison
equal deleted inserted replaced
1:983ff3800d7f 2:085625ddf82c
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$dist" dist.dat && 13 ln -s '$dist' dist.dat &&
14 ln -s "$name" name.dat && 14 ln -s '$name' name.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 16
17 echo 'cluster.classic( 17 echo 'cluster.classic(
18 phylip=dist.dat, 18 phylip=dist.dat,
19 #if $name: 19 #if $name:
20 name=name.dat, 20 name=name.dat,
21 #end if 21 #end if
22 #if $count: 22 #if $count:
23 count=count.dat, 23 count=count.dat,
24 #end if 24 #end if
25 method=$method, 25 method=$method,
26 #if $cutoff: 26 #if $cutoff:
27 cutoff=$cutoff, 27 cutoff=$cutoff,
28 #end if 28 #end if
29 hard=$hard, 29 precision=$precision,
30 precision=$precision, 30 sim=$sim
31 sim=$sim 31 )'
32 )' 32 | sed 's/ //g' ## mothur trips over whitespace
33 | sed 's/ //g' ## mothur trips over whitespace 33 | mothur
34 | mothur 34 | tee mothur.out.log
35 | tee mothur.out.log
36 ]]></command> 35 ]]></command>
37 <inputs> 36 <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"/> 37 <param argument="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"
39 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 38 help="format must be mothur.lower.dist or mothur.square.dist"/>
40 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 39 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
41 <param name="method" type="select" label="method - Select a Clustering Method" help=""> 40 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
41 <param argument="method" type="select" label="method - Select a Clustering Method" help="">
42 <option value="furthest">Furthest neighbor</option> 42 <option value="furthest">Furthest neighbor</option>
43 <option value="nearest">Nearest neighbor</option> 43 <option value="nearest">Nearest neighbor</option>
44 <option value="average" selected="true">Average neighbor</option> 44 <option value="average" selected="true">Average neighbor</option>
45 <option value="weighted">Weighted</option> 45 <option value="weighted">Weighted</option>
46 </param> 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"/> 47 <param argument="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold"
48 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/> 48 help="Ignore pairwise distances larger than this. Default for methods opti,agc,dgc is 0.03, default for the other methods is 0.15"/>
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"> 49 <param argument="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
50 help="Set higher precision for longer genome scale sequence lengths">
50 <option value="10">.1</option> 51 <option value="10">.1</option>
51 <option value="100" selected="true">.01</option> 52 <option value="100" selected="true">.01</option>
52 <option value="1000">.001</option> 53 <option value="1000">.001</option>
53 <option value="10000">.0001</option> 54 <option value="10000">.0001</option>
54 <option value="100000">.00001</option> 55 <option value="100000">.00001</option>
55 <option value="1000000">.000001</option> 56 <option value="1000000">.000001</option>
56 </param> 57 </param>
57 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/> 58 <param argument="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
59 <expand macro="param-savelog"/>
58 </inputs> 60 </inputs>
59 <outputs> 61 <outputs>
60 <expand macro="logfile-output"/> 62 <expand macro="logfile-output"/>
61 <data name="rabund" format="mothur.rabund" from_work_dir="dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> 63 <data name="rabund" format="mothur.rabund" from_work_dir="dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
62 <data name="sabund" format="mothur.sabund" from_work_dir="dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> 64 <data name="sabund" format="mothur.sabund" from_work_dir="dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
72 <has_text text="group"/> 74 <has_text text="group"/>
73 <has_text text="unique"/> 75 <has_text text="unique"/>
74 <has_line_matching expression="^label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24$"/> 76 <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> 77 </assert_contents>
76 </output> 78 </output>
79 <param name="savelog" value="true"/>
77 <expand macro="logfile-test"/> 80 <expand macro="logfile-test"/>
78 </test> 81 </test>
79 </tests> 82 </tests>
80 <help> 83 <help><![CDATA[
81 <![CDATA[
82 84
83 @MOTHUR_OVERVIEW@ 85 @MOTHUR_OVERVIEW@
84 86
85 **Command Documentation** 87 **Command Documentation**
86 88
87 The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit). 89 The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit).
88 90
89 .. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic 91 .. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic
90 92
91 ]]> 93 ]]></help>
92 </help>
93 <expand macro="citations"/> 94 <expand macro="citations"/>
94 </tool> 95 </tool>