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comparison hcluster.xml @ 0:e5faf9bdcbbe 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 16:35:04 -0400
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-1:000000000000 0:e5faf9bdcbbe
1 <tool profile="16.07" id="mothur_hcluster" name="Hcluster" 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
13 echo 'hcluster(
14 #if $matrix.format == "column":
15 column=matrix.dist.dat,
16 name=matrix.name.dat,
17 #elif $matrix.format == "phylip":
18 phylip=matrix.dist.dat,
19 #if $matrix.name:
20 name=matrix.name.dat,
21 #end if
22 #end if
23 method=$method,
24 #if $cutoff:
25 cutoff=$cutoff,
26 #end if
27 precision=$precision,
28 hard=$hard,
29 sorted=$sorted,
30 showabund=$showabund
31 )'
32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur
34 ]]></command>
35 <inputs>
36 <conditional name="matrix">
37 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
38 <option value="column">Pairwise Column Matrix</option>
39 <option value="phylip">Phylip Distance Matrix</option>
40 </param>
41 <when value="column">
42 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
43 <param name="name" type="data" format="mothur.names" label="name - Names"/>
44 </when>
45 <when value="phylip">
46 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
47 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
48 </when>
49 </conditional>
50 <param name="cutoff" type="float" value="" min="0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
51 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
52 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
53 <option value="10">.1</option>
54 <option value="100" selected="true">.01</option>
55 <option value="1000">.001</option>
56 <option value="10000">.0001</option>
57 <option value="100000">.00001</option>
58 <option value="1000000">.000001</option>
59 </param>
60 <param name="method" type="select" label="method - Select a Clustering Method" help="">
61 <option value="average" selected="true">Average neighbor</option>
62 <option value="nearest">Nearest neighbor</option>
63 <option value="furthest">Furthest neighbor</option>
64 <option value="weighted">Weighted</option>
65 </param>
66 <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - The input matrix is already sorted"/>
67 <param name="showabund" type="boolean" checked="true" truevalue="true" falsevalue="false" label="showabund - Verbose ouput"/>
68 </inputs>
69 <outputs>
70 <expand macro="logfile-output"/>
71 <data name="rabund" format="mothur.rabund" from_work_dir="matrix.dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
72 <data name="sabund" format="mothur.sabund" from_work_dir="matrix.dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
73 <data name="otulist" format="mothur.list" from_work_dir="matrix.dist*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
74 </outputs>
75 <tests>
76 <test><!-- test with phylip input-->
77 <param name="format" value="phylip"/>
78 <param name="dist" value="98_sq_phylip_amazon.dist"/>
79 <output name="rabund" md5="aafe1357a2f76e2d05e52c5a26838061" ftype="mothur.rabund"/>
80 <output name="sabund" md5="103af393a98579aec05e3cc935343a3c" ftype="mothur.sabund"/>
81 <output name="otulist" ftype="mothur.list">
82 <assert_contents>
83 <has_text text="unique"/>
84 <has_text text="label"/>
85 <has_text text="numOtus"/>
86 <has_text text="Otu98"/>
87 </assert_contents>
88 </output>
89 <expand macro="logfile-test"/>
90 </test>
91 <test><!-- test with column and name input -->
92 <param name="format" value="column"/>
93 <param name="dist" value="amazon.pair.dist"/>
94 <param name="name" value="amazon.names"/>
95 <output name="rabund" md5="ec88216404729d0f4a0463e50e60c9ad" ftype="mothur.rabund"/>
96 <output name="sabund" md5="f2c714531430b98d8cdfd3497468eec2" ftype="mothur.sabund"/>
97 <output name="otulist" ftype="mothur.list">
98 <assert_contents>
99 <has_text text="unique"/>
100 <has_text text="label"/>
101 <has_text text="numOtus"/>
102 <has_text text="Otu96"/>
103 </assert_contents>
104 </output>
105 <expand macro="logfile-test"/>
106 </test>
107 </tests>
108 <help>
109 <![CDATA[
110
111 @MOTHUR_OVERVIEW@
112
113 **Command Documenation**
114
115 The hcluster_ 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.
116
117 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
118 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
119 .. _name: http://www.mothur.org/wiki/Name_file
120 .. _list: http://www.mothur.org/wiki/List_file
121 .. _rabund: http://www.mothur.org/wiki/Rabund_file
122 .. _sabund: http://www.mothur.org/wiki/Sabund_file
123 .. _hcluster: http://www.mothur.org/wiki/Hcluster
124
125 ]]>
126 </help>
127 <expand macro="citations"/>
128 </tool>