Mercurial > repos > iuc > mothur_get_sharedseqs

comparison get.sharedseqs.xml @ 2:d5b97213e4ba 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 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:23:51 -0400
parents 1d496917a707
children ea2e9c5e62b9
comparison
equal deleted inserted replaced
1:a441bf009014 2:d5b97213e4ba
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 "$infile.otu" infile_otu.dat && 13 ln -s '$infile.otu' infile_otu.dat &&
14 #if $infile.intype == "in_listgroup": 14 #if $infile.intype == "in_listgroup":
15 ln -s "$infile.group" infile.group.dat && 15 ln -s '$infile.group' infile.group.dat &&
16 ln -s "$infile.fasta" infile_fasta.dat && 16 ln -s '$infile.fasta' infile_fasta.dat &&
17 ln -s '$count_in' count_in.dat &&
18 #end if
19
20 echo 'get.sharedseqs(
21 #if $infile.intype == "in_listgroup":
22 list=infile_otu.dat
23
24 #if $group:
25 ,group=infile.group.dat
26 #elif $count_in:
27 ,count=count_in.dat
17 #end if 28 #end if
18 29
19 echo 'get.sharedseqs( 30 #if $infile.fasta:
20 #if $infile.intype == "in_listgroup": 31 ,fasta=infile_fasta.dat
21 list=infile_otu.dat 32 #end if
22 ,group=infile.group.dat 33 #else
23 #if $infile.fasta: 34 shared=infile_otu.dat
24 ,fasta=infile_fasta.dat 35 #end if
25 #end if 36 #if $infile.label:
26 #else 37 ,label=${ str($infile.label).replace(",","-") }
27 shared=infile_otu.dat 38 #end if
28 #end if 39 #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups:
29 #if $infile.label: 40 ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") }
30 ,label=${ str($infile.label).replace(",","-") } 41 #end if
31 #end if 42 #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups:
32 #if $infile.seqsfrom.selection == "unique" and $infile.seqsfrom.groups: 43 ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") }
33 ,uniquegroups=${ str($infile.seqsfrom.groups).replace(",","-") } 44 #end if
34 #end if 45 #if $output:
35 #if $infile.seqsfrom.selection == "shared" and $infile.seqsfrom.groups: 46 ,output=$output
36 ,sharedgroups=${ str($infile.seqsfrom.groups).replace(",","-") } 47 #end if
37 #end if 48 )'
38 #if $output: 49 | sed 's/ //g' ## mothur trips over whitespace
39 ,output=$output 50 | mothur
40 #end if 51 | tee mothur.out.log
41 )'
42 | sed 's/ //g' ## mothur trips over whitespace
43 | mothur
44 | tee mothur.out.log
45 ]]></command> 52 ]]></command>
46 <inputs> 53 <inputs>
47 <conditional name="infile"> 54 <conditional name="infile">
48 <param name="intype" type="select" label="Will you be supplying a shared file or a list and group file?" help=""> 55 <param name="intype" type="select" label="Will you be supplying a shared file or a list and group file?" help="">
49 <option value="in_shared">Shared file</option> 56 <option value="in_shared">Shared file</option>
79 <when value="all"/> 86 <when value="all"/>
80 </conditional> 87 </conditional>
81 </when> 88 </when>
82 <when value="in_listgroup"> 89 <when value="in_listgroup">
83 <param name="otu" type="data" format="mothur.list" label="list - OTU List or shared file"/> 90 <param name="otu" type="data" format="mothur.list" label="list - OTU List or shared file"/>
84 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels to include" help="By default all are included if no selection is made"> 91 <param name="label" type="select" optional="true" multiple="true" label="label - Select OTU Labels to include"
92 help="By default all are included if no selection is made">
85 <options> 93 <options>
86 <filter type="data_meta" ref="otu" key="labels"/> 94 <filter type="data_meta" ref="otu" key="labels"/>
87 </options> 95 </options>
88 </param> 96 </param>
89 <param name="group" type="data" format="mothur.groups" optional="true" label="group - not required if using a shared file"/> 97 <param name="group" type="data" format="mothur.groups" optional="true" label="group - not required if using a shared file"/>
90 <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset" help="will output a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified"/> 98 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
99 <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset"
100 help="will output a fasta file for each distance level containing only the sequences that are in OTUs shared by the groups specified"/>
91 <conditional name="seqsfrom"> 101 <conditional name="seqsfrom">
92 <param name="selection" type="select" label="Select Groups" help=""> 102 <param name="selection" type="select" label="Select Groups" help="">
93 <option value="all" selected="true">None (use all groups)</option> 103 <option value="all" selected="true">None (use all groups)</option>
94 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option> 104 <option value="unique">OTUs that contain ONLY sequences from the selected groups</option>
95 <option value="shared">OTUs that contain sequences from the selected groups</option> 105 <option value="shared">OTUs that contain sequences from the selected groups</option>
114 </conditional> 124 </conditional>
115 <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs"> 125 <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs">
116 <option value="" selected="true">default: (name group bin_number)</option> 126 <option value="" selected="true">default: (name group bin_number)</option>
117 <option value="accnos">accnos (name)</option> 127 <option value="accnos">accnos (name)</option>
118 </param> 128 </param>
129 <expand macro="param-savelog"/>
119 </inputs> 130 </inputs>
120 <outputs> 131 <outputs>
121 <expand macro="logfile-output"/> 132 <expand macro="logfile-output"/>
122 <collection name="sharedseqs" type="list" label="${tool.name} on ${on_string}: shared.seqs"> 133 <collection name="sharedseqs" type="list" label="${tool.name} on ${on_string}: shared.seqs">
123 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.seqs" format="tabular"/> 134 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared\.seqs" format="tabular"/>
136 <test><!-- test with shared file --> 147 <test><!-- test with shared file -->
137 <param name="intype" value="in_shared"/> 148 <param name="intype" value="in_shared"/>
138 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 149 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
139 <param name="selection" value="shared"/> 150 <param name="selection" value="shared"/>
140 <output_collection name="sharedseqs" count="35"> 151 <output_collection name="sharedseqs" count="35">
141 <element name="0.41.unique.forest-pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/> 152 <element name="0.41.unique.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
142 </output_collection> 153 </output_collection>
154 <param name="savelog" value="true"/>
143 <expand macro="logfile-test"/> 155 <expand macro="logfile-test"/>
144 </test> 156 </test>
145 <test><!-- test with list and group file --> 157 <test><!-- test with list and group file -->
146 <param name="intype" value="in_listgroup"/> 158 <param name="intype" value="in_listgroup"/>
147 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 159 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
148 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 160 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
149 <output_collection name="sharedseqs" count="35"> 161 <output_collection name="sharedseqs" count="35">
150 <element name="0.41.unique.forest-pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/> 162 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
151 </output_collection> 163 </output_collection>
164 <param name="savelog" value="true"/>
152 <expand macro="logfile-test"/> 165 <expand macro="logfile-test"/>
153 </test> 166 </test>
154 <test><!-- test with shared seqs and subset of labels --> 167 <test><!-- test with shared seqs and subset of labels -->
155 <param name="intype" value="in_shared"/> 168 <param name="intype" value="in_shared"/>
156 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 169 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
157 <param name="selection" value="shared"/> 170 <param name="selection" value="shared"/>
158 <param name="groups" value="forest,pasture"/> 171 <param name="groups" value="forest,pasture"/>
159 <param name="label" value="0.03,0.33,0.41"/> 172 <param name="label" value="0.03,0.33,0.41"/>
160 <output_collection name="sharedseqs" count="3"> 173 <output_collection name="sharedseqs" count="3">
161 <element name="0.41.forest-pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/> 174 <element name="0.41.forest_pasture" md5="e07fe8acfa12d6f61a9efee88d91be54" ftype="tabular"/>
162 </output_collection> 175 </output_collection>
176 <param name="savelog" value="true"/>
163 <expand macro="logfile-test"/> 177 <expand macro="logfile-test"/>
164 </test> 178 </test>
165 <test><!-- test with unique seqs and subset of groups --> 179 <test><!-- test with unique seqs and subset of groups -->
166 <param name="intype" value="in_shared"/> 180 <param name="intype" value="in_shared"/>
167 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 181 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
168 <param name="selection" value="unique"/> 182 <param name="selection" value="unique"/>
169 <param name="groups" value="pasture"/> 183 <param name="groups" value="pasture"/>
170 <output_collection name="sharedseqs" count="34"> 184 <output_collection name="sharedseqs" count="34">
171 <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/> 185 <element name="0.41.unique.pasture" md5="f4735f56d96d13cd603ca0b11c4bc231" ftype="tabular"/>
172 </output_collection> 186 </output_collection>
187 <param name="savelog" value="true"/>
173 <expand macro="logfile-test"/> 188 <expand macro="logfile-test"/>
174 </test> 189 </test>
175 <test><!-- test with accnos output --> 190 <test><!-- test with accnos output -->
176 <param name="intype" value="in_shared"/> 191 <param name="intype" value="in_shared"/>
177 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 192 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
178 <param name="output" value="accnos"/> 193 <param name="output" value="accnos"/>
179 <output_collection name="sharedaccnos" count="35"> 194 <output_collection name="sharedaccnos" count="35">
180 <element name="0.41.unique.forest-pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/> 195 <element name="0.41.unique.forest_pasture" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.accnos"/>
181 </output_collection> 196 </output_collection>
197 <param name="savelog" value="true"/>
182 <expand macro="logfile-test"/> 198 <expand macro="logfile-test"/>
183 </test> 199 </test>
184 <test><!-- test with fasta input and output --> 200 <test><!-- test with fasta input and output -->
185 <param name="intype" value="in_listgroup"/> 201 <param name="intype" value="in_listgroup"/>
186 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 202 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
187 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 203 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
188 <param name="fasta" value="amazon.fasta" ftype="fasta"/> 204 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
189 <output_collection name="sharedseqs" count="35"> 205 <output_collection name="sharedseqs" count="35">
190 <element name="0.41.unique.forest-pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/> 206 <element name="0.41.unique.forest_pasture" md5="ceb32c3dc2c99055efdaa6ef6aaed7f0" ftype="tabular"/>
191 </output_collection> 207 </output_collection>
192 <output_collection name="sharedfastas" count="35"> 208 <output_collection name="sharedfastas" count="35">
193 <element name="0.41.unique.forest-pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/> 209 <element name="0.41.unique.forest_pasture" md5="fd4265d7c139d2d3acf8e19e6337ee28" ftype="fasta"/>
194 </output_collection> 210 </output_collection>
211 <param name="savelog" value="true"/>
195 <expand macro="logfile-test"/> 212 <expand macro="logfile-test"/>
196 </test> 213 </test>
197 </tests> 214 </tests>
198 <help> 215 <help><![CDATA[
199 <![CDATA[
200 216
201 @MOTHUR_OVERVIEW@ 217 @MOTHUR_OVERVIEW@
202 218
203 **Command Documentation** 219 **Command Documentation**
204 220
205 The get.sharedseqs_ command takes a list and group file and outputs a .shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify. 221 The get.sharedseqs_ command takes a list and group file and outputs a .shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify.
206 222
207 .. _get.sharedseqs: https://www.mothur.org/wiki/Get.sharedseqs 223 .. _get.sharedseqs: https://www.mothur.org/wiki/Get.sharedseqs
208 224
209 v1.21.0: Updated to Mothur 1.33, added shared file option 225 v1.21.0: Updated to Mothur 1.33, added shared file option
210 ]]> 226
211 </help> 227 ]]></help>
212 <expand macro="citations"/> 228 <expand macro="citations"/>
213 </tool> 229 </tool>