Mercurial > repos > iuc > mothur_cluster_split

comparison cluster.split.xml @ 2:3c24b99497db 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 22:16:50 -0400
parents e70a33ec8f3b
children 2c02989afecb
comparison
equal deleted inserted replaced
1:a29ac7993cb0 2:3c24b99497db
1 <tool profile="16.07" id="mothur_cluster_split" name="Cluster.split" version="@WRAPPER_VERSION@.0"> 1 <tool profile="16.07" id="mothur_cluster_split" name="Cluster.split" version="@WRAPPER_VERSION@.0">
2 <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description> 2 <description>Assign sequences to OTUs and split large matrices</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 <requirement type="package" version="2.6.0">vsearch</requirement>
8 </expand>
7 <expand macro="stdio"/> 9 <expand macro="stdio"/>
8 <expand macro="version_command"/> 10 <expand macro="version_command"/>
9 <command><![CDATA[ 11 <command><![CDATA[
10 @SHELL_OPTIONS@ 12 @SHELL_OPTIONS@
11 13
12 ## create symlinks to input datasets 14 ## create symlinks to input datasets
13 #if $splitby.splitmethod == "distance": 15 #if $splitby.splitmethod == "distance":
14 ln -s "$splitby.matrix.dist" splitby.matrix.dist.dat && 16 ln -s '$splitby.matrix.dist' splitby.matrix.dist.dat &&
15 ln -s "$splitby.matrix.nameOrCount" splitby.matrix.nameOrCount.dat && 17 ln -s '$splitby.matrix.nameOrCount' splitby.matrix.nameOrCount.dat &&
16 #elif $splitby.splitmethod == "classify": 18 #elif $splitby.splitmethod == "classify":
17 ln -s "$splitby.dist" splitby.dist.dat && 19 ln -s '$splitby.dist' splitby.dist.dat &&
18 ln -s "$splitby.nameOrCount" splitby.nameOrCount.dat && 20 ln -s '$splitby.nameOrCount' splitby.nameOrCount.dat &&
19 ln -s "$splitby.taxonomy" splitby.taxonomy.dat && 21 ln -s '$splitby.taxonomy' splitby.taxonomy.dat &&
20 #elif $splitby.splitmethod == "fasta": 22 #elif $splitby.splitmethod == "fasta":
21 ln -s "$splitby.fasta" splitby.fasta.dat && 23 ln -s '$splitby.fasta' splitby.fasta.dat &&
22 ln -s "$splitby.nameOrCount" splitby.nameOrCount.dat && 24 ln -s '$splitby.nameOrCount' splitby.nameOrCount.dat &&
23 ln -s "$splitby.taxonomy" splitby.taxonomy.dat && 25 ln -s '$splitby.taxonomy' splitby.taxonomy.dat &&
24 #end if 26 #end if
25 27
26 echo 'cluster.split( 28 echo 'cluster.split(
27 splitmethod=$splitby.splitmethod, 29 splitmethod=$splitby.splitmethod,
28 #if $splitby.splitmethod == "distance": 30 #if $splitby.splitmethod == "distance":
29 #if $splitby.matrix.format == "column": 31 #if $splitby.matrix.format == "column":
30 column=splitby.matrix.dist.dat, 32 column=splitby.matrix.dist.dat,
31 #if $splitby.matrix.nameOrCount.is_of_type("mothur.names"): 33 #if $splitby.matrix.nameOrCount.is_of_type("mothur.names"):
32 name=splitby.matrix.nameOrCount.dat, 34 name=splitby.matrix.nameOrCount.dat,
33 #elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"): 35 #elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"):
34 count=splitby.matrix.nameOrCount.dat, 36 count=splitby.matrix.nameOrCount.dat,
35 #end if 37 #end if
36 #elif $splitby.matrix.format == "phylip": 38 #elif $splitby.matrix.format == "phylip":
37 phylip=splitby.matrix.dist.dat, 39 phylip=splitby.matrix.dist.dat,
38 #if $splitby.matrix.nameOrCount: 40 #if $splitby.matrix.nameOrCount:
39 #if $splitby.matrix.nameOrCount.is_of_type("mothur.names"): 41 #if $splitby.matrix.nameOrCount.is_of_type("mothur.names"):
40 name=splitby.matrix.nameOrCount.dat, 42 name=splitby.matrix.nameOrCount.dat,
41 #elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"): 43 #elif $splitby.matrix.nameOrCount.is_of_type("mothur.count_table"):
42 count=splitby.matrix.nameOrCount.dat, 44 count=splitby.matrix.nameOrCount.dat,
43 #end if
44 #end if
45 #end if 45 #end if
46 #elif $splitby.splitmethod == "classify":
47 column=splitby.dist.dat,
48 taxonomy=splitby.taxonomy.dat,
49 #if $splitby.nameOrCount.is_of_type("mothur.names"):
50 name=splitby.nameOrCount.dat,
51 #elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
52 count=splitby.nameOrCount.dat,
53 #end if
54 #if $splitby.taxlevel:
55 taxlevel=$splitby.taxlevel,
56 #end if
57 #elif $splitby.splitmethod == "fasta":
58 fasta=splitby.fasta.dat,
59 taxonomy=splitby.taxonomy.dat,
60 #if $splitby.nameOrCount.is_of_type("mothur.names"):
61 name=splitby.nameOrCount.dat,
62 #elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
63 count=splitby.nameOrCount.dat,
64 #end if
65 #if $splitby.taxlevel:
66 taxlevel=$splitby.taxlevel,
67 #end if
68 classic=$splitby.classic,
69 #end if 46 #end if
70 #if $method: 47 #end if
71 method=$method, 48 #elif $splitby.splitmethod == "classify":
72 #end if 49 column=splitby.dist.dat,
73 #if float($cutoff) > 0.0: 50 taxonomy=splitby.taxonomy.dat,
74 cutoff=$cutoff, 51 #if $splitby.nameOrCount.is_of_type("mothur.names"):
75 #end if 52 name=splitby.nameOrCount.dat,
76 hard=$hard, 53 #elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
77 #if $precision 54 count=splitby.nameOrCount.dat,
78 precision=$precision, 55 #end if
79 #end if 56 #if $splitby.taxlevel:
80 large=$large, 57 taxlevel=$splitby.taxlevel,
81 cluster=$cluster, 58 #end if
82 processors='\${GALAXY_SLOTS:-8}' 59 #elif $splitby.splitmethod == "fasta":
83 )' 60 fasta=splitby.fasta.dat,
84 | sed 's/ //g' ## mothur trips over whitespace 61 taxonomy=splitby.taxonomy.dat,
85 | mothur 62 #if $splitby.nameOrCount.is_of_type("mothur.names"):
86 | tee mothur.out.log 63 name=splitby.nameOrCount.dat,
64 #elif $splitby.nameOrCount.is_of_type("mothur.count_table"):
65 count=splitby.nameOrCount.dat,
66 #end if
67 #if $splitby.taxlevel:
68 taxlevel=$splitby.taxlevel,
69 #end if
70 classic=$splitby.classic,
71 #end if
72 method=$splitby.condmethod.method,
73 #if $splitby.condmethod.method == "opti":
74 metric=$splitby.condmethod.metric,
75 initialize=$splitby.condmethod.initialize,
76 delta=$splitby.condmethod.delta,
77 iters=$splitby.condmethod.iters,
78 #end if
79 #if float($cutoff) > 0.0:
80 cutoff=$cutoff,
81 #end if
82 #if $precision
83 precision=$precision,
84 #end if
85 large=$large,
86 cluster=$cluster,
87 runsensspec=$runsensspec,
88 processors='\${GALAXY_SLOTS:-8}'
89 )'
90 | sed 's/ //g' ## mothur trips over whitespace
91 | mothur
92 | tee mothur.out.log
87 ]]></command> 93 ]]></command>
88 <inputs> 94 <inputs>
89 <conditional name="splitby"> 95 <conditional name="splitby">
90 <param name="splitmethod" type="select" label="Split by" help=""> 96 <param name="splitmethod" type="select" label="Split by" help="VSEARCH methods (agc and dgc) require a fasta file">
91 <option value="distance">Distance</option> 97 <option value="distance">Distance</option>
92 <option value="classify">Classification</option> 98 <option value="classify">Classification</option>
93 <option value="fasta">Classification using fasta</option> 99 <option value="fasta">Classification using fasta</option>
94 </param> 100 </param>
95 <when value="distance"> 101 <when value="distance">
96 <conditional name="matrix"> 102 <conditional name="matrix">
97 <param name="format" type="select" label="Select a Distance Matrix Format" help=""> 103 <param name="format" type="select" label="Select a Distance Matrix Format">
98 <option value="column">Pairwise Column Matrix</option> 104 <option value="column">Pairwise Column Matrix</option>
99 <option value="phylip">Phylip Distance Matrix</option> 105 <option value="phylip">Phylip Distance Matrix</option>
100 </param> 106 </param>
101 <when value="column"> 107 <when value="column">
102 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> 108 <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
103 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/> 109 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
104 </when> 110 </when>
105 <when value="phylip"> 111 <when value="phylip">
106 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 112 <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
107 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Name reference"/> 113 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="name file or count table - Sequences Name reference"/>
114 </when>
115 </conditional>
116 <conditional name="condmethod">
117 <expand macro="param-clustermethods"/>
118 <when value="furthest"/>
119 <when value="nearest"/>
120 <when value="average"/>
121 <when value="opti">
122 <expand macro="params-opticlust"/>
108 </when> 123 </when>
109 </conditional> 124 </conditional>
110 </when> 125 </when>
111 <when value="classify"> 126 <when value="classify">
112 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> 127 <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
113 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/> 128 <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
114 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/> 129 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
115 <param name="taxlevel" type="integer" value="1" min="1" label="taxlevel - taxonomy level for split (default=1)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> 130 <param argument="taxlevel" type="integer" value="1" min="1" label="taxlevel - taxonomy level for split (default=1)"
131 help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
132 <conditional name="condmethod">
133 <expand macro="param-clustermethods"/>
134 <when value="furthest"/>
135 <when value="nearest"/>
136 <when value="average"/>
137 <when value="opti">
138 <expand macro="params-opticlust"/>
139 </when>
140 </conditional>
116 </when> 141 </when>
117 <when value="fasta"> 142 <when value="fasta">
118 <param name="fasta" type="data" format="mothur.align,fasta" label="fasta - Aligned Sequences" help="must be aligned sequences (mothur.align)"/> 143 <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta"/>
119 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/> 144 <param argument="taxonomy" type="data" format="mothur.seq.taxonomy" label="Taxonomy" help="can be obtained by running classify.seqs"/>
120 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/> 145 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
121 <param name="taxlevel" type="integer" value="3" min="1" label="taxlevel - taxonomy level for split (default=3)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> 146 <param argument="taxlevel" type="integer" value="3" min="1" label="taxlevel - taxonomy level for split (default=3)"
122 <param name="classic" type="boolean" checked="false" truevalue="true" falsevalue="false" label="classic - Use cluster.classic"/> 147 help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
148 <param argument="classic" type="boolean" checked="false" truevalue="true" falsevalue="false" label="classic - Use cluster.classic"/>
149 <conditional name="condmethod">
150 <expand macro="param-clustermethods">
151 <expand macro="option-vsearch-clustermethods"/>
152 </expand>
153 <when value="furthest"/>
154 <when value="nearest"/>
155 <when value="average"/>
156 <when value="agc"/>
157 <when value="dgc"/>
158 <when value="opti">
159 <expand macro="params-opticlust"/>
160 </when>
161 </conditional>
123 </when> 162 </when>
124 </conditional> 163 </conditional>
125 <param name="method" type="select" label="method - Select a Clustering Method" help=""> 164 <param argument="cutoff" type="float" value="0.0" min="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0"
126 <option value="furthest">Furthest neighbor</option> 165 help="Ignore pairwise distances larger than this, a common value would be 0.25"/>
127 <option value="nearest">Nearest neighbor</option> 166 <param argument="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
128 <option value="average" selected="true">Average neighbor</option> 167 help="Set higher precision for longer genome scale sequence lengths">
129 </param>
130 <param name="cutoff" type="float" value="0.0" min="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.25"/>
131 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding" help=""/>
132 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths">
133 <option value="10">.1</option> 168 <option value="10">.1</option>
134 <option value="100" selected="true">.01</option> 169 <option value="100" selected="true">.01</option>
135 <option value="1000">.001</option> 170 <option value="1000">.001</option>
136 <option value="10000">.0001</option> 171 <option value="10000">.0001</option>
137 <option value="100000">.00001</option> 172 <option value="100000">.00001</option>
138 <option value="1000000">.000001</option> 173 <option value="1000000">.000001</option>
139 </param> 174 </param>
140 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - distance matrix is too large to fit in RAM" help="If your job fails due to not enough memory error, set this to true to rerun"/> 175 <param argument="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - distance matrix is too large to fit in RAM"
141 <param name="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="The cluster parameter allows you to indicate whether you want to run the clustering or just split the distance matrix, default=T"/> 176 help="If your job fails due to not enough memory error, set this to true to rerun"/>
177 <param argument="cluster" type="boolean" falsevalue="false" truevalue="true" checked="true" label="perform clustering?"
178 help="indicate whether you want to run the clustering or just split the distance matrix"/>
179 <param argument="runsensspec" type="boolean" truevalue="true" falsevalue="false" checked="true" label="runsensspec" help="run the sens.spec command on the completed list file"/>
180 <expand macro="param-savelog"/>
142 </inputs> 181 </inputs>
143 <outputs> 182 <outputs>
144 <expand macro="logfile-output"/> 183 <expand macro="logfile-output"/>
145 <data name="rabund" format="mothur.rabund" from_work_dir="splitby.*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"> 184 <data name="rabund" format="mothur.rabund" from_work_dir="splitby.*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)">
146 <filter>splitby['nameOrCount'].ext != "mothur.count_table"</filter> 185 <filter>splitby['nameOrCount'].ext != "mothur.count_table"</filter>
160 <discover_datasets pattern=".*?\.names\.(?P&lt;designation&gt;.*)\.temp" format="mothur.names"/> 199 <discover_datasets pattern=".*?\.names\.(?P&lt;designation&gt;.*)\.temp" format="mothur.names"/>
161 </collection> 200 </collection>
162 <data name="splitfile" format="txt" from_work_dir="splitby.*.file" label="${tool.name} on ${on_string}: split.file"> 201 <data name="splitfile" format="txt" from_work_dir="splitby.*.file" label="${tool.name} on ${on_string}: split.file">
163 <filter>not cluster</filter> 202 <filter>not cluster</filter>
164 </data> 203 </data>
204 <data name="sensspec" format="txt" from_work_dir="splitby.*.sensspec" label="${tool.name} on ${on_string}: sensspec">
205 <filter>runsensspec and splitby['condmethod']['method'] == "opti"</filter>
206 </data>
165 </outputs> 207 </outputs>
166 <tests> 208 <tests>
167 <test><!-- test with distance method --> 209 <test><!-- test with distance method -->
168 <param name="splitmethod" value="distance"/> 210 <param name="splitmethod" value="distance"/>
169 <param name="format" value="phylip"/> 211 <param name="format" value="phylip"/>
170 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> 212 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
171 <output name="otulist" md5="2613ef0a1805ba9de012a41e938d8947" ftype="mothur.list"/> 213 <param name="method" value="average"/>
172 <output name="rabund" md5="4df813ec2d51c373a846a82380c7a1f8" ftype="mothur.rabund"/> 214 <output name="otulist" ftype="mothur.list">
173 <output name="sabund" md5="8d6813a5e8d2ad426a0ee5fdd99f1a19" ftype="mothur.sabund"/> 215 <assert_contents>
216 <expand macro="test-list-format"/>
217 <has_text text="unique"/>
218 <has_text text="U68680"/>
219 </assert_contents>
220 </output>
221 <output name="rabund" ftype="mothur.rabund">
222 <assert_contents>
223 <has_line_matching expression="^unique(\t\d+)+$"/>
224 <has_text text="0.03"/>
225 </assert_contents>
226 </output>
227 <output name="sabund" ftype="mothur.sabund">
228 <assert_contents>
229 <has_line_matching expression="^unique(\t\d+)+$"/>
230 <has_text text="0.03"/>
231 </assert_contents>
232 </output>
233 <param name="savelog" value="true"/>
174 <expand macro="logfile-test"/> 234 <expand macro="logfile-test"/>
175 </test> 235 </test>
176 <test><!-- test with cluster false --> 236 <test><!-- test with cluster false -->
177 <param name="splitmethod" value="distance"/> 237 <param name="splitmethod" value="distance"/>
178 <param name="format" value="phylip"/> 238 <param name="format" value="phylip"/>
179 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> 239 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
180 <param name="cluster" value="false"/> 240 <param name="cluster" value="false"/>
241 <param name="method" value="average"/>
181 <output name="splitfile" ftype="txt"> 242 <output name="splitfile" ftype="txt">
182 <assert_contents> 243 <assert_contents>
183 <has_text text="column"/> 244 <has_text text="column"/>
184 <has_text text="dist"/> 245 <has_text text="dist"/>
185 <has_text text="names"/> 246 <has_text text="names"/>
186 <has_text text="temp"/> 247 <has_text text="temp"/>
187 </assert_contents> 248 </assert_contents>
188 </output> 249 </output>
189 <output_collection name="splitnames" count="4"> 250 <output_collection name="splitnames" count="14">
190 <element name="0" md5="27037eeb3e696888b24653d0996261cd" ftype="mothur.names"/> 251 <element name="0" ftype="mothur.names">
252 <assert_contents>
253 <has_text text="U68591"/>
254 <has_text text="U68600"/>
255 </assert_contents>
256 </element>
191 </output_collection> 257 </output_collection>
192 <output_collection name="splitdist" count="3"> 258 <output_collection name="splitdist" count="13">
193 <element name="4" md5="f751aee00b598d3b6691d34f67dbc8d5" ftype="mothur.dist"/> 259 <element name="4" ftype="mothur.dist">
260 <assert_contents>
261 <has_line_matching expression="^U\d+\tU\d+\t\d+\.\d+$"/>
262 </assert_contents>
263 </element>
194 </output_collection> 264 </output_collection>
265 <param name="savelog" value="true"/>
195 <expand macro="logfile-test"/> 266 <expand macro="logfile-test"/>
196 </test> 267 </test>
197 <test><!-- test with classify method (mothur.names input file) --> 268 <test><!-- test with classify method (mothur.names input file) -->
198 <param name="splitmethod" value="classify"/> 269 <param name="splitmethod" value="classify"/>
199 <param name="format" value="column"/> 270 <param name="format" value="column"/>
200 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/> 271 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
201 <param name="nameOrCount" value="amazon.names" ftype="mothur.names"/> 272 <param name="nameOrCount" value="amazon.names" ftype="mothur.names"/>
202 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 273 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
274 <param name="method" value="average"/>
203 <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/> 275 <output name="otulist" md5="d6eba624ad79759c530b9bc3285a1361" ftype="mothur.list"/>
204 <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/> 276 <output name="rabund" md5="2a165e1e40644fccb8cc9f53d8915bc3" ftype="mothur.rabund"/>
205 <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/> 277 <output name="sabund" md5="7aad8a9ca0eade414d6eba1f8bef960f" ftype="mothur.sabund"/>
278 <param name="savelog" value="true"/>
206 <expand macro="logfile-test"/> 279 <expand macro="logfile-test"/>
207 </test> 280 </test>
208 <test><!-- test with classify method (mothur.count_table input file) --> 281 <test><!-- test with classify method (mothur.count_table input file) -->
209 <param name="splitmethod" value="classify"/> 282 <param name="splitmethod" value="classify"/>
210 <param name="format" value="column"/> 283 <param name="format" value="column"/>
211 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/> 284 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
212 <param name="nameOrCount" value="amazon.count_table" ftype="mothur.count_table"/> 285 <param name="nameOrCount" value="amazon.count_table" ftype="mothur.count_table"/>
213 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 286 <param name="taxonomy" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
287 <param name="method" value="average"/>
214 <output name="otulist" md5="c5c28330434d3e773221f635d04d6af9" ftype="mothur.list"/> 288 <output name="otulist" md5="c5c28330434d3e773221f635d04d6af9" ftype="mothur.list"/>
289 <param name="savelog" value="true"/>
215 <expand macro="logfile-test"/> 290 <expand macro="logfile-test"/>
216 </test> 291 </test>
217 <test><!-- test with fasta --> 292 <test><!-- test with fasta -->
218 <param name="splitmethod" value="fasta"/> 293 <param name="splitmethod" value="fasta"/>
219 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/> 294 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
220 <param name="nameOrCount" value="amazon.align_head.names" ftype="mothur.names"/> 295 <param name="nameOrCount" value="amazon.align_head.names" ftype="mothur.names"/>
221 <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/> 296 <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
222 <param name="cutoff" value="9999"/> 297 <param name="cutoff" value="9999"/>
298 <param name="method" value="average"/>
223 <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/> 299 <output name="otulist" md5="a1279248cf2bc1094e0046b2cff1b785" ftype="mothur.list"/>
224 <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/> 300 <output name="rabund" md5="65ec9f326cd92fc607679b9902ec8430" ftype="mothur.rabund"/>
225 <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/> 301 <output name="sabund" md5="854d3acd15f64299c5d9d9e18f2d51b4" ftype="mothur.sabund"/>
302 <param name="savelog" value="true"/>
303 <expand macro="logfile-test"/>
304 </test>
305 <test><!-- test with vsearch executable (agc/dgc method) -->
306 <param name="splitmethod" value="fasta"/>
307 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
308 <param name="nameOrCount" value="amazon.align_head.names" ftype="mothur.names"/>
309 <param name="taxonomy" value="amazon.align_head.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
310 <param name="method" value="agc"/>
311 <output name="otulist" md5="0fbc5bf21331538dd50b6586c4005edc" ftype="mothur.list"/>
312 <output name="rabund" md5="dcccca11d9fa7a186cd93e9d4592f832" ftype="mothur.rabund"/>
313 <output name="sabund" md5="167815924b1b2b4d4e5e7468d41256cb" ftype="mothur.sabund"/>
314 <param name="savelog" value="true"/>
315 <expand macro="logfile-test"/>
316 </test>
317 <test><!-- test with opticlust method -->
318 <param name="splitmethod" value="distance"/>
319 <param name="format" value="phylip"/>
320 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
321 <param name="method" value="opti"/>
322 <output name="otulist" ftype="mothur.list">
323 <assert_contents>
324 <expand macro="test-list-format"/>
325 <has_text text="0.03"/>
326 </assert_contents>
327 </output>
328 <output name="rabund" ftype="mothur.rabund">
329 <assert_contents>
330 <expand macro="test-rabund-format"/>
331 <has_text text="0.03"/>
332 </assert_contents>
333 </output>
334 <output name="sabund" ftype="mothur.sabund">
335 <assert_contents>
336 <expand macro="test-sabund-format"/>
337 <has_text text="0.03"/>
338 </assert_contents>
339 </output>
340 <output name="sensspec" ftype="txt">
341 <assert_contents>
342 <expand macro="test-sensspec-format"/>
343 <has_text text="0.03"/>
344 </assert_contents>
345 </output>
346 <param name="savelog" value="true"/>
226 <expand macro="logfile-test"/> 347 <expand macro="logfile-test"/>
227 </test> 348 </test>
228 </tests> 349 </tests>
229 <help> 350 <help><![CDATA[
230 <![CDATA[
231 351
232 @MOTHUR_OVERVIEW@ 352 @MOTHUR_OVERVIEW@
233 353
234 354
235 **Command Documentation** 355 **Command Documentation**
238 358
239 .. _cluster.split: https://www.mothur.org/wiki/Cluster.split 359 .. _cluster.split: https://www.mothur.org/wiki/Cluster.split
240 360
241 v1.28.0: Upgraded to Mothur 1.33, introduced cluster boolean. 361 v1.28.0: Upgraded to Mothur 1.33, introduced cluster boolean.
242 362
243 ]]> 363 ]]></help>
244 </help>
245 <expand macro="citations"/> 364 <expand macro="citations"/>
246 </tool> 365 </tool>