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comparison hcluster.xml @ 1:db21b211d44c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:46:34 -0400
parents e5faf9bdcbbe
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0:e5faf9bdcbbe 1:db21b211d44c
2 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> 2 <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$matrix.dist" matrix.dist.dat && 13 ln -s "$matrix.dist" matrix.dist.dat &&
11 ln -s "$matrix.name" matrix.name.dat && 14 ln -s "$matrix.name" matrix.name.dat &&
12 15
13 echo 'hcluster( 16 echo 'hcluster(
29 sorted=$sorted, 32 sorted=$sorted,
30 showabund=$showabund 33 showabund=$showabund
31 )' 34 )'
32 | sed 's/ //g' ## mothur trips over whitespace 35 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur 36 | mothur
37 | tee mothur.out.log
34 ]]></command> 38 ]]></command>
35 <inputs> 39 <inputs>
36 <conditional name="matrix"> 40 <conditional name="matrix">
37 <param name="format" type="select" label="Select a Distance Matrix Format" help=""> 41 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
38 <option value="column">Pairwise Column Matrix</option> 42 <option value="column">Pairwise Column Matrix</option>
41 <when value="column"> 45 <when value="column">
42 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> 46 <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"/> 47 <param name="name" type="data" format="mothur.names" label="name - Names"/>
44 </when> 48 </when>
45 <when value="phylip"> 49 <when value="phylip">
46 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 50 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
47 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/> 51 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
48 </when> 52 </when>
49 </conditional> 53 </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"/> 54 <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"/> 55 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
74 </outputs> 78 </outputs>
75 <tests> 79 <tests>
76 <test><!-- test with phylip input--> 80 <test><!-- test with phylip input-->
77 <param name="format" value="phylip"/> 81 <param name="format" value="phylip"/>
78 <param name="dist" value="98_sq_phylip_amazon.dist"/> 82 <param name="dist" value="98_sq_phylip_amazon.dist"/>
79 <output name="rabund" md5="aafe1357a2f76e2d05e52c5a26838061" ftype="mothur.rabund"/> 83 <output name="rabund" ftype="mothur.rabund">
80 <output name="sabund" md5="103af393a98579aec05e3cc935343a3c" ftype="mothur.sabund"/> 84 <assert_contents>
85 <has_line_matching expression="0\.[0-9]+(\t[0-9]+)+"/>
86 </assert_contents>
87 </output>
88 <output name="sabund" ftype="mothur.sabund">
89 <assert_contents>
90 <has_line_matching expression="0\.[0-9]+(\t[0-9]+)+"/>
91 </assert_contents>
92 </output>
81 <output name="otulist" ftype="mothur.list"> 93 <output name="otulist" ftype="mothur.list">
82 <assert_contents> 94 <assert_contents>
83 <has_text text="unique"/> 95 <has_text text="unique"/>
84 <has_text text="label"/> 96 <has_text text="label"/>
85 <has_text text="numOtus"/> 97 <has_text text="numOtus"/>
108 <help> 120 <help>
109 <![CDATA[ 121 <![CDATA[
110 122
111 @MOTHUR_OVERVIEW@ 123 @MOTHUR_OVERVIEW@
112 124
113 **Command Documenation** 125 **Command Documentation**
114 126
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. 127 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.
116 128
117 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix 129 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
118 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix 130 .. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix
119 .. _name: http://www.mothur.org/wiki/Name_file 131 .. _name: https://www.mothur.org/wiki/Name_file
120 .. _list: http://www.mothur.org/wiki/List_file 132 .. _list: https://www.mothur.org/wiki/List_file
121 .. _rabund: http://www.mothur.org/wiki/Rabund_file 133 .. _rabund: https://www.mothur.org/wiki/Rabund_file
122 .. _sabund: http://www.mothur.org/wiki/Sabund_file 134 .. _sabund: https://www.mothur.org/wiki/Sabund_file
123 .. _hcluster: http://www.mothur.org/wiki/Hcluster
124 135
125 ]]> 136 ]]>
126 </help> 137 </help>
127 <expand macro="citations"/> 138 <expand macro="citations"/>
128 </tool> 139 </tool>