Mercurial > repos > iuc > mothur_get_oturep

comparison get.oturep.xml @ 0:d568050a95be draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:33:26 -0400
parents
children 17b63c3cc04d
comparison
equal deleted inserted replaced
-1:000000000000 0:d568050a95be
1 <tool profile="16.07" id="mothur_get_oturep" name="Get.oturep" version="@WRAPPER_VERSION@.0">
2 <description>Generate a fasta with a representative sequence for each OTU</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11 ln -s "$fasta" fasta.dat &&
12 ln -s "$input.dist" input.dist.dat &&
13 ln -s "$input.name" input.name.dat &&
14 ln -s "$count" count.dat &&
15 #if $pick.type == "yes":
16 ln -s "$pick.group" pick.group.dat &&
17 #end if
18
19 echo 'get.oturep(
20 list=otu.dat,
21 #if $fasta:
22 fasta=fasta.dat,
23 #end if
24 #if $input.source == "column":
25 column=input.dist.dat,
26 name=input.name.dat,
27 #elif $input.source == "phylip":
28 phylip=input.dist.dat,
29 #if $input.name:
30 name=input.name.dat,
31 #end if
32 #end if
33 #if $label:
34 label=${ str($label).replace(",","-") },
35 #end if
36 #if $pick.type == "yes":
37 #if $pick.group:
38 group=pick.group.dat,
39 #end if
40 #if $pick.groups:
41 groups=${ str($pick.groups).replace(",","-") },
42 #end if
43 #end if
44 #if $sorted:
45 sorted=$sorted,
46 #end if
47 #if $count and not $input.name:
48 count=count.dat,
49 #end if
50 method=$method,
51 large=$large
52 )'
53 | sed 's/ //g' ## mothur trips over whitespace
54 | mothur
55 ]]></command>
56 <inputs>
57 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
58 <conditional name="input">
59 <param name="source" type="select" label="Distance Matrix Format">
60 <option value="column">Pairwise Column Distance Matrix</option>
61 <option value="phylip">Phylip Distance Matrix</option>
62 </param>
63 <when value="column">
64 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
65 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
66 </when>
67 <when value="phylip">
68 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
69 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
70 </when>
71 </conditional>
72 <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Fasta"/>
73 <conditional name="pick">
74 <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
75 <option value="no" selected="true">No</option>
76 <option value="yes">Yes</option>
77 </param>
78 <when value="no"/>
79 <when value="yes">
80 <param name="group" type="data" format="mothur.groups" label="group - Group file for the OTU List"/>
81 <param name="groups" type="select" multiple="true" label="groups - Group Selection (all used if none are selected)">
82 <options>
83 <filter type="data_meta" ref="group" key="groups"/>
84 </options>
85 </param>
86 </when>
87 </conditional>
88 <param name="label" type="select" multiple="true" label="label - OTU Labels">
89 <expand macro="labeloptions"/>
90 </param>
91 <param name="sorted" type="select" label="sorted - Sort Sequences by">
92 <option value="">Don't sort</option>
93 <option value="name">Sequence Name</option>
94 <option value="number">Bin Number</option>
95 <option value="size">Bin Size</option>
96 <option value="group">Group</option>
97 </param>
98 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Distance Matrix is very Large"/>
99 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="Cannot supply both a names and count table. Will be ignored if you also supplied a name file. Generated by count.seqs"/>
100 <param name="method" type="select" label="method - select the method of selecting the representative sequence" help="the distance method finds the sequence with the smallest maximum distance to other sequences. The abundance method chooses the abundant sequence in the OTU as the representative. Default=distance">
101 <option value="distance" selected="true">distance</option>
102 <option value="abundance">abundance</option>
103 </param>
104 </inputs>
105 <outputs>
106 <expand macro="logfile-output"/>
107 <collection name="names_out" type="list" label="${tool.name} on ${on_string}: rep.names">
108 <filter>input['name'] or not count</filter>
109 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.names" format="mothur.names"/>
110 </collection>
111 <collection name="fasta_out" type="list" label="${tool.name} on ${on_string}: rep.fasta">
112 <filter>fasta</filter>
113 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.fasta" format="fasta"/>
114 </collection>
115 <collection name="count_out" type="list" label="${tool.name} on ${on_string}: rep.count_table">
116 <filter>count and not input['name']</filter>
117 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.rep\.count_table" format="mothur.count_table"/>
118 </collection>
119 </outputs>
120 <tests>
121 <test><!-- test with phylip -->
122 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
123 <param name="source" value="phylip"/>
124 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
125 <param name="name" value="amazon1.names" ftype="mothur.names"/>
126 <output_collection name="names_out" count="36">
127 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
128 </output_collection>
129 <expand macro="logfile-test"/>
130 </test>
131 <test><!-- test with column and label select -->
132 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
133 <param name="source" value="column"/>
134 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
135 <param name="name" value="amazon1.names" ftype="mothur.names"/>
136 <param name="label" value="unique,0.05,0.27,0.45"/>
137 <output_collection name="names_out" count="4">
138 <element name="0.27" md5="be6dccdd3d4619c3ac465246c826209a" ftype="mothur.names"/>
139 </output_collection>
140 <expand macro="logfile-test"/>
141 </test>
142 <test><!-- test with fasta and sorting-->
143 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
144 <param name="source" value="phylip"/>
145 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
146 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
147 <param name="label" value="0.05,0.27"/>
148 <param name="sorted" value="name"/>
149 <output_collection name="names_out" count="2">
150 <element name="0.27" md5="39ff2858909d49633871d5a625585de5" ftype="mothur.names"/>
151 </output_collection>
152 <output_collection name="fasta_out" count="2">
153 <element name="0.27" md5="a9d9622b6f5fcbe8acdc05df5484ffc4" ftype="fasta"/>
154 </output_collection>
155 <expand macro="logfile-test"/>
156 </test>
157 <test><!-- test with group file -->
158 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
159 <param name="source" value="column"/>
160 <param name="dist" value="amazon.pair.dist" ftype="mothur.pair.dist"/>
161 <param name="name" value="amazon1.names" ftype="mothur.names"/>
162 <param name="label" value="unique,0.05,0.27,0.45"/>
163 <param name="type" value="yes"/>
164 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
165 <param name="groups" value="forest,pasture"/>
166 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/> <!-- should be ignored as we also supplied name file -->
167 <output_collection name="names_out" count="8">
168 <element name="0.27.pasture" md5="34f87d93fd9ebbefed9754f627f502fd" ftype="mothur.names"/>
169 </output_collection>
170 <expand macro="logfile-test"/>
171 </test>
172 <test><!-- test with count table -->
173 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
174 <param name="source" value="phylip"/>
175 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
176 <param name="label" value="unique,0.05,0.27"/>
177 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
178 <output_collection name="count_out" count="3">
179 <element name="0.27" md5="6b1afd712825af4bf8cb4ab8304df903" ftype="mothur.count_table"/>
180 </output_collection>
181 <expand macro="logfile-test"/>
182 </test>
183 </tests>
184 <help>
185 <![CDATA[
186
187 @MOTHUR_OVERVIEW@
188
189
190 **Command Documenation**
191
192 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.
193
194 .. _get.oturep: http://www.mothur.org/wiki/Get.oturep
195
196 v1.23.0: Updated to Mothur 1.33, added count and method parameter
197 ]]>
198 </help>
199 <expand macro="citations"/>
200 </tool>