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comparison cluster.xml @ 2:6f2cdccbfa48 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 22:08:08 -0400
parents 8c1b609f566d
children 3bb756df109c
comparison
equal deleted inserted replaced
1:2834e2dd0d61 2:6f2cdccbfa48
1 <tool profile="16.07" id="mothur_cluster" name="Cluster" version="@WRAPPER_VERSION@.0"> 1 <tool profile="16.07" id="mothur_cluster" name="Cluster" version="@WRAPPER_VERSION@.0">
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 <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 ln -s "$matrix.dist" matrix.dist.dat && 15 ln -s '$matrix.dist' matrix.dist.dat &&
14 ln -s "$matrix.name" matrix.name.dat && 16 ln -s '$matrix.name' matrix.name.dat &&
15 ln -s "$count" count.dat && 17 ln -s '$count' count.dat &&
16 18
17 echo 'cluster( 19 echo 'cluster(
18 #if $matrix.format == "phylip": 20 #if $matrix.format == "phylip":
19 phylip=matrix.dist.dat, 21 phylip=matrix.dist.dat,
20 #else 22 #else
21 column=matrix.dist.dat, 23 column=matrix.dist.dat,
22 #end if 24 #end if
23 #if $matrix.name: 25 #if $matrix.name:
24 name=matrix.name.dat, 26 name=matrix.name.dat,
25 #end if 27 #end if
26 #if $count: 28 #if $count:
27 count=count.dat, 29 count=count.dat,
28 #end if 30 #end if
29 hard=$hard, 31 #if float($cutoff) > 0.0:
30 #if float($cutoff) > 0.0: 32 cutoff=$cutoff,
31 cutoff=$cutoff, 33 #end if
32 #end if 34 #if $select_method.method =="opti":
33 precision=$precision, 35 metric=$select_method.metric,
34 sim=$sim, 36 initialize=$select_method.initialize,
35 method=$method 37 delta=$select_method.delta,
36 )' 38 iters=$select_method.iters,
37 | sed 's/ //g' ## mothur trips over whitespace 39 #end if
38 | mothur 40 precision=$precision,
39 | tee mothur.out.log 41 sim=$sim,
42 method=$select_method.method
43 )'
44 | sed 's/ //g' ## mothur trips over whitespace
45 | mothur
46 | tee mothur.out.log
40 ]]></command> 47 ]]></command>
41 <inputs> 48 <inputs>
42 <conditional name="matrix"> 49 <conditional name="matrix">
43 <param name="format" type="select" label="Select a Distance Matrix Format" help=""> 50 <param name="format" type="select" label="Cluster based on" help="">
44 <option value="column">Pairwise Column Matrix</option> 51 <option value="column">Pairwise Column Matrix</option>
45 <option value="phylip">Phylip Distance Matrix</option> 52 <option value="phylip">Phylip Distance Matrix</option>
53 <option value="fasta">Fasta (VSEARCH)</option>
46 </param> 54 </param>
47 <when value="column"> 55 <when value="column">
48 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> 56 <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
49 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 57 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
50 </when> 58 </when>
51 <when value="phylip"> 59 <when value="phylip">
52 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 60 <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
53 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 61 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
62 </when>
63 <when value="fasta">
64 <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta file"/>
54 </when> 65 </when>
55 </conditional> 66 </conditional>
56 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 67 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
57 <param name="method" type="select" label="method - Select a Clustering Method" help=""> 68 <conditional name="select_method">
58 <option value="furthest">Furthest neighbor</option> 69 <expand macro="param-clustermethods">
59 <option value="nearest">Nearest neighbor</option> 70 <expand macro="option-vsearch-clustermethods"/>
60 <option value="average" selected="true">Average neighbor</option> 71 </expand>
61 <option value="weighted">Weighted</option> 72 <when value="furthest"/>
62 </param> 73 <when value="nearest"/>
63 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0.0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/> 74 <when value="average"/>
64 <param name="hard" type="boolean" checked="true" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/> 75 <when value="agc">
65 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths"> 76 <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta file"/>
77 </when>
78 <when value="dgc">
79 <param argument="fasta" type="data" format="mothur.align,fasta" label="Fasta file"/>
80 </when>
81 <when value="opti">
82 <expand macro="params-opticlust"/>
83 </when>
84 </conditional>
85 <param argument="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0.0"
86 help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
87 <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
88 help="Set higher precision for longer genome scale sequence lengths">
66 <option value="10">.1</option> 89 <option value="10">.1</option>
67 <option value="100" selected="true">.01</option> 90 <option value="100" selected="true">.01</option>
68 <option value="1000">.001</option> 91 <option value="1000">.001</option>
69 <option value="10000">.0001</option> 92 <option value="10000">.0001</option>
70 <option value="100000">.00001</option> 93 <option value="100000">.00001</option>
71 <option value="1000000">.000001</option> 94 <option value="1000000">.000001</option>
72 </param> 95 </param>
73 <param name="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/> 96 <param argument="sim" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sim - Matrix values are Similary instead of Distance"/>
97 <expand macro="param-savelog"/>
74 </inputs> 98 </inputs>
75 <outputs> 99 <outputs>
76 <expand macro="logfile-output"/> 100 <expand macro="logfile-output"/>
77 <data name="rabund" format="mothur.rabund" from_work_dir="matrix.dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> 101 <data name="rabund" format="mothur.rabund" from_work_dir="matrix.dist*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
78 <data name="sabund" format="mothur.sabund" from_work_dir="matrix.dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> 102 <data name="sabund" format="mothur.sabund" from_work_dir="matrix.dist*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
80 </outputs> 104 </outputs>
81 <tests> 105 <tests>
82 <test><!-- test with phylip input --> 106 <test><!-- test with phylip input -->
83 <param name="format" value="phylip"/> 107 <param name="format" value="phylip"/>
84 <param name="dist" value="amazon.dist"/> 108 <param name="dist" value="amazon.dist"/>
85 <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/> 109 <output name="rabund" ftype="mothur.rabund">
86 <output name="sabund" file="amazon.an.sabund" ftype="mothur.sabund"/> 110 <assert_contents>
87 <output name="otulist" md5="a6bf2a6ef7950b3ee2aa5bff4a662b6d" ftype="mothur.list"/> 111 <has_line_matching expression="^0\.03(\t\d+)+$"/>
112 </assert_contents>
113 </output>
114 <output name="sabund" ftype="mothur.sabund">
115 <assert_contents>
116 <has_line_matching expression="^0\.03(\t\d+)+$"/>
117 </assert_contents>
118 </output>
119 <output name="otulist" ftype="mothur.list">
120 <assert_contents>
121 <expand macro="test-list-format"/>
122 <has_text text="0.03"/>
123 <has_text text="U68688"/>
124 </assert_contents>
125 </output>
126 <param name="savelog" value="true"/>
88 <expand macro="logfile-test"/> 127 <expand macro="logfile-test"/>
89 </test> 128 </test>
90 <test><!-- test with column input --> 129 <test><!-- test with column input -->
91 <param name="format" value="column"/> 130 <param name="format" value="column"/>
92 <param name="dist" value="amazon.pair.dist"/> 131 <param name="dist" value="amazon.pair.dist"/>
93 <param name="name" value="amazon.names"/> 132 <param name="name" value="amazon.names"/>
94 <output name="rabund" md5="ec88216404729d0f4a0463e50e60c9ad" ftype="mothur.rabund"/> 133 <output name="rabund" ftype="mothur.rabund">
95 <output name="sabund" md5="f2c714531430b98d8cdfd3497468eec2" ftype="mothur.sabund"/> 134 <assert_contents>
96 <output name="otulist" md5="1769463ed0b6680babe5801bf9c0a85c" ftype="mothur.list"/> 135 <has_line_matching expression="^0\.03(\t\d+)+$"/>
136 </assert_contents>
137 </output>
138 <output name="sabund" ftype="mothur.sabund">
139 <assert_contents>
140 <has_line_matching expression="^0\.03(\t\d+)+$"/>
141 </assert_contents>
142 </output>
143 <output name="otulist" ftype="mothur.list">
144 <assert_contents>
145 <expand macro="test-list-format"/>
146 <has_text text="0.03"/>
147 <has_text text="U68688"/>
148 </assert_contents>
149 </output>
150 <param name="savelog" value="true"/>
151 <expand macro="logfile-test"/>
152 </test>
153 <test><!-- test with column input -->
154 <param name="format" value="column"/>
155 <param name="dist" value="amazon.pair.dist"/>
156 <param name="name" value="amazon.names"/>
157 <output name="rabund" ftype="mothur.rabund">
158 <assert_contents>
159 <has_line_matching expression="^0\.03(\t\d+)+$"/>
160 </assert_contents>
161 </output>
162 <output name="sabund" ftype="mothur.sabund">
163 <assert_contents>
164 <has_line_matching expression="^0\.03(\t\d+)+$"/>
165 </assert_contents>
166 </output>
167 <output name="otulist" ftype="mothur.list">
168 <assert_contents>
169 <expand macro="test-list-format"/>
170 <has_text text="0.03"/>
171 <has_text text="U68688"/>
172 </assert_contents>
173 </output>
174 <param name="savelog" value="true"/>
97 <expand macro="logfile-test"/> 175 <expand macro="logfile-test"/>
98 </test> 176 </test>
99 </tests> 177 </tests>
100 <help> 178 <help><![CDATA[
101 <![CDATA[
102 179
103 @MOTHUR_OVERVIEW@ 180 @MOTHUR_OVERVIEW@
104 181
105 **Command Documentation** 182 **Command Documentation**
106 183
112 .. _list: https://www.mothur.org/wiki/List_file 189 .. _list: https://www.mothur.org/wiki/List_file
113 .. _rabund: https://www.mothur.org/wiki/Rabund_file 190 .. _rabund: https://www.mothur.org/wiki/Rabund_file
114 .. _sabund: https://www.mothur.org/wiki/Sabund_file 191 .. _sabund: https://www.mothur.org/wiki/Sabund_file
115 .. _cluster: https://www.mothur.org/wiki/Cluster 192 .. _cluster: https://www.mothur.org/wiki/Cluster
116 193
117 ]]> 194 ]]></help>
118 </help>
119 <expand macro="citations"/> 195 <expand macro="citations"/>
120 </tool> 196 </tool>