Mercurial > repos > iuc > mothur_get_oturep

comparison get.oturep.xml @ 2:07d536eabf6c 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 22:11:51 -0400
parents e6758f2f744b
children
comparison
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1:92e175ba0032 2:07d536eabf6c
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 "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 #if $method_condition.method_switch == "distance": 14 #if $method_condition.method_switch == "distance":
15 ln -s "$method_condition.matrix_condition.dist" dist.dat && 15 ln -s '$method_condition.matrix_condition.dist' dist.dat &&
16 ln -s "$method_condition.matrix_condition.nameOrCount" nameOrCount.dat && 16 ln -s '$method_condition.matrix_condition.nameOrCount' nameOrCount.dat &&
17 ln -s "$method_condition.fasta" fasta.dat && 17 ln -s '$method_condition.fasta' fasta.dat &&
18 #if $method_condition.pick.type == "yes": 18 #if $method_condition.pick.type == "yes":
19 ln -s "$method_condition.pick.group" group.dat && 19 ln -s '$method_condition.pick.group' group.dat &&
20 #end if 20 #end if
21 #elif $method_condition.method_switch == "abundance": 21 #elif $method_condition.method_switch == "abundance":
22 ln -s "$method_condition.nameOrCount" nameOrCount.dat && 22 ln -s '$method_condition.nameOrCount' nameOrCount.dat &&
23 #end if 23 #end if
24 24
25 echo 'get.oturep( 25 echo 'get.oturep(
26 list=otu.dat, 26 list=otu.dat,
27 #if $sorted: 27 #if $sorted:
28 sorted=$sorted, 28 sorted=$sorted,
29 #end if 29 #end if
30 #if $label: 30 #if $label:
31 label=${ str($label).replace(",","-") }, 31 label=${ str($label).replace(",","-") },
32 #end if 32 #end if
33 #if $method_condition.method_switch == "distance": 33 #if $method_condition.method_switch == "distance":
34 method=distance, 34 method=distance,
35 #if $method_condition.matrix_condition.matrix_format == "column": 35 #if $method_condition.matrix_condition.matrix_format == "column":
36 column=dist.dat, 36 column=dist.dat,
37 #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"): 37 #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
38 name=nameOrCount.dat, 38 name=nameOrCount.dat,
39 #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"): 39 #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
40 count=nameOrCount.dat, 40 count=nameOrCount.dat,
41 #end if 41 #end if
42 #elif $method_condition.matrix_condition.matrix_format == "phylip": 42 #elif $method_condition.matrix_condition.matrix_format == "phylip":
43 phylip=dist.dat, 43 phylip=dist.dat,
44 #if $method_condition.matrix_condition.nameOrCount: 44 #if $method_condition.matrix_condition.nameOrCount:
45 #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"): 45 #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
46 name=nameOrCount.dat, 46 name=nameOrCount.dat,
47 #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"): 47 #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
48 count=nameOrCount.dat, 48 count=nameOrCount.dat,
49 #end if
50 #end if
51 #end if 49 #end if
52 #if $method_condition.fasta: 50 #end if
53 fasta=fasta.dat, 51 #end if
54 #end if 52 #if $method_condition.fasta:
55 #if $method_condition.pick.type == "yes": 53 fasta=fasta.dat,
56 #if $method_condition.pick.group: 54 #end if
57 group=group.dat, 55 #if $method_condition.pick.type == "yes":
58 #end if 56 #if $method_condition.pick.group:
59 #if $method_condition.pick.groups: 57 group=group.dat,
60 groups=${ str($method_condition.pick.groups).replace(",","-") }, 58 #end if
61 #end if 59 #if $method_condition.pick.groups:
62 #end if 60 groups=${ str($method_condition.pick.groups).replace(",","-") },
63 large=$method_condition.large 61 #end if
64 #elif $method_condition.method_switch == "abundance": 62 #end if
65 method=abundance, 63 large=$method_condition.large
66 #if $method_condition.nameOrCount.is_of_type("mothur.names"): 64 #elif $method_condition.method_switch == "abundance":
67 name=nameOrCount.dat 65 method=abundance,
68 #elif $method_condition.nameOrCount.is_of_type("mothur.count_table"): 66 #if $method_condition.nameOrCount.is_of_type("mothur.names"):
69 count=nameOrCount.dat 67 name=nameOrCount.dat
70 #end if 68 #elif $method_condition.nameOrCount.is_of_type("mothur.count_table"):
71 #end if 69 count=nameOrCount.dat
72 )' 70 #end if
73 | sed 's/ //g' ## mothur trips over whitespace 71 #end if
74 | mothur 72 )'
75 | tee mothur.out.log 73 | sed 's/ //g' ## mothur trips over whitespace
74 | mothur
75 | tee mothur.out.log
76 ]]></command> 76 ]]></command>
77 <inputs> 77 <inputs>
78 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 78 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
79 <conditional name="method_condition"> 79 <conditional name="method_condition">
80 <param name="method_switch" type="select" label="Method to use for the selection of the representative sequences" help="The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the most abundant sequence in the OTU as the representative."> 80 <param name="method_switch" type="select" label="Method to use for the selection of the representative sequences"
81 help="The distance method finds the sequence with the smallest maximum distance to other sequences. The abundance
82 method chooses the most abundant sequence in the OTU as the representative.">
81 <option value="distance" selected="true">distance</option> 83 <option value="distance" selected="true">distance</option>
82 <option value="abundance">abundance</option> 84 <option value="abundance">abundance</option>
83 </param> 85 </param>
84 <when value="distance"> 86 <when value="distance">
85 <conditional name="matrix_condition"> 87 <conditional name="matrix_condition">
110 <filter type="data_meta" ref="group" key="groups"/> 112 <filter type="data_meta" ref="group" key="groups"/>
111 </options> 113 </options>
112 </param> 114 </param>
113 </when> 115 </when>
114 </conditional> 116 </conditional>
115 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large" help="Set this parameter to Yes if your distance matric might not fit in RAM"/> 117 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large"
118 help="Set this parameter to Yes if your distance matric might not fit in RAM"/>
116 </when> 119 </when>
117 <when value="abundance"> 120 <when value="abundance">
118 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/> 121 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="name file or count table - Sequences Name reference"/>
119 </when> 122 </when>
120 </conditional> 123 </conditional>
126 <option value="name">Sequence Name</option> 129 <option value="name">Sequence Name</option>
127 <option value="number">Bin Number</option> 130 <option value="number">Bin Number</option>
128 <option value="size">Bin Size</option> 131 <option value="size">Bin Size</option>
129 <option value="group">Group</option> 132 <option value="group">Group</option>
130 </param> 133 </param>
134 <expand macro="param-savelog"/>
131 </inputs> 135 </inputs>
132 <outputs> 136 <outputs>
133 <expand macro="logfile-output"/> 137 <expand macro="logfile-output"/>
134 <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names"> 138 <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names">
135 <filter>method_condition['nameOrCount'].ext == "mothur.names"</filter> 139 <filter>method_condition['nameOrCount'].ext == "mothur.names"</filter>
156 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> 160 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
157 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/> 161 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/>
158 <output_collection name="names_out" count="36"> 162 <output_collection name="names_out" count="36">
159 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/> 163 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
160 </output_collection> 164 </output_collection>
165 <param name="savelog" value="true"/>
161 <expand macro="logfile-test"/> 166 <expand macro="logfile-test"/>
162 </test> 167 </test>
163 <!-- test with distance / column / label select --> 168 <!-- test with distance / column / label select -->
164 <test> 169 <test>
165 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 170 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
169 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/> 174 <param name="nameOrCount" value="amazon1.names" ftype="mothur.names"/>
170 <param name="label" value="unique,0.05,0.27,0.45"/> 175 <param name="label" value="unique,0.05,0.27,0.45"/>
171 <output_collection name="names_out" count="4"> 176 <output_collection name="names_out" count="4">
172 <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/> 177 <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/>
173 </output_collection> 178 </output_collection>
179 <param name="savelog" value="true"/>
174 <expand macro="logfile-test"/> 180 <expand macro="logfile-test"/>
175 </test> 181 </test>
176 <!-- test with distance / fasta / sorting --> 182 <!-- test with distance / fasta / sorting -->
177 <test> 183 <test>
178 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 184 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
186 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/> 192 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
187 </output_collection> 193 </output_collection>
188 <output_collection name="fasta_out" count="2"> 194 <output_collection name="fasta_out" count="2">
189 <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/> 195 <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/>
190 </output_collection> 196 </output_collection>
197 <param name="savelog" value="true"/>
191 <expand macro="logfile-test"/> 198 <expand macro="logfile-test"/>
192 </test> 199 </test>
193 <!-- test with distance / group file --> 200 <!-- test with distance / group file -->
194 <test> 201 <test>
195 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 202 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
202 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 209 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
203 <param name="groups" value="forest,pasture"/> 210 <param name="groups" value="forest,pasture"/>
204 <output_collection name="names_out" count="8"> 211 <output_collection name="names_out" count="8">
205 <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/> 212 <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/>
206 </output_collection> 213 </output_collection>
214 <param name="savelog" value="true"/>
207 <expand macro="logfile-test"/> 215 <expand macro="logfile-test"/>
208 </test> 216 </test>
209 <!-- test with distance / count table --> 217 <!-- test with distance / count table -->
210 <test> 218 <test>
211 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 219 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
215 <param name="label" value="unique,0.05,0.27"/> 223 <param name="label" value="unique,0.05,0.27"/>
216 <param name="nameOrCount" value="amazon1.count_table" ftype="mothur.count_table"/> 224 <param name="nameOrCount" value="amazon1.count_table" ftype="mothur.count_table"/>
217 <output_collection name="count_out" count="3"> 225 <output_collection name="count_out" count="3">
218 <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/> 226 <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/>
219 </output_collection> 227 </output_collection>
228 <param name="savelog" value="true"/>
220 <expand macro="logfile-test"/> 229 <expand macro="logfile-test"/>
221 </test> 230 </test>
222 <!-- test with abundance / count / label --> 231 <!-- test with abundance / count / label -->
223 <!-- It seems that the content of the result file can vary from one execution to another with the same parameters --> 232 <!-- It seems that the content of the result file can vary from one execution to another with the same parameters -->
224 <test> 233 <test>
232 <assert_contents> 241 <assert_contents>
233 <has_text_matching expression="U68\w+\t36" /> 242 <has_text_matching expression="U68\w+\t36" />
234 </assert_contents> 243 </assert_contents>
235 </element> 244 </element>
236 </output_collection> 245 </output_collection>
246 <param name="savelog" value="true"/>
237 <expand macro="logfile-test"/> 247 <expand macro="logfile-test"/>
238 </test> 248 </test>
239 </tests> 249 </tests>
240 <help> 250 <help><![CDATA[
241 <![CDATA[
242 251
243 @MOTHUR_OVERVIEW@ 252 @MOTHUR_OVERVIEW@
244 253
245 254
246 **Command Documentation** 255 **Command Documentation**
248 The get.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. The opposite of the bin.seqs command. 257 The get.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. The opposite of the bin.seqs command.
249 258
250 .. _get.oturep: https://www.mothur.org/wiki/Get.oturep 259 .. _get.oturep: https://www.mothur.org/wiki/Get.oturep
251 260
252 v1.23.0: Updated to Mothur 1.33, added count and method parameter 261 v1.23.0: Updated to Mothur 1.33, added count and method parameter
253 ]]> 262
254 </help> 263 ]]></help>
255 <expand macro="citations"/> 264 <expand macro="citations"/>
256 </tool> 265 </tool>