Mercurial > repos > iuc > mothur_get_oturep

comparison get.oturep.xml @ 3:899ef1660676 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:44:01 -0500
parents 17b63c3cc04d
children 2ac0e471b97a
comparison
equal deleted inserted replaced
2:d3e59b8d2921 3:899ef1660676
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>
235 </element> 238 </element>
236 </output_collection> 239 </output_collection>
237 <expand macro="logfile-test"/> 240 <expand macro="logfile-test"/>
238 </test> 241 </test>
239 </tests> 242 </tests>
240 <help> 243 <help><![CDATA[
241 <![CDATA[
242 244
243 @MOTHUR_OVERVIEW@ 245 @MOTHUR_OVERVIEW@
244 246
245 247
246 **Command Documentation** 248 **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. 250 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.
249 251
250 .. _get.oturep: https://www.mothur.org/wiki/Get.oturep 252 .. _get.oturep: https://www.mothur.org/wiki/Get.oturep
251 253
252 v1.23.0: Updated to Mothur 1.33, added count and method parameter 254 v1.23.0: Updated to Mothur 1.33, added count and method parameter
253 ]]> 255
254 </help> 256 ]]></help>
255 <expand macro="citations"/> 257 <expand macro="citations"/>
256 </tool> 258 </tool>