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comparison get.sharedseqs.xml @ 1:e4e0bfb92a94 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:49:35 -0400
parents d20133cb8909
children 30f2529d9cc6
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0:d20133cb8909 1:e4e0bfb92a94
2 <description>Get shared sequences at each distance from list and group</description> 2 <description>Get shared sequences at each distance from list and group</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 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$infile.otu" infile_otu.dat && 13 ln -s "$infile.otu" infile_otu.dat &&
11 #if $infile.intype == "in_listgroup": 14 #if $infile.intype == "in_listgroup":
12 ln -s "$infile.group" infile.group.dat && 15 ln -s "$infile.group" infile.group.dat &&
13 ln -s "$infile.fasta" infile_fasta.dat && 16 ln -s "$infile.fasta" infile_fasta.dat &&
36 ,output=$output 39 ,output=$output
37 #end if 40 #end if
38 )' 41 )'
39 | sed 's/ //g' ## mothur trips over whitespace 42 | sed 's/ //g' ## mothur trips over whitespace
40 | mothur 43 | mothur
44 | tee mothur.out.log
41 ]]></command> 45 ]]></command>
42 <inputs> 46 <inputs>
43 <conditional name="infile"> 47 <conditional name="infile">
44 <param name="intype" type="select" label="Will you be supplying a shared file or a list and group file?" help=""> 48 <param name="intype" type="select" label="Will you be supplying a shared file or a list and group file?" help="">
45 <option value="in_shared">Shared file</option> 49 <option value="in_shared">Shared file</option>
194 <help> 198 <help>
195 <![CDATA[ 199 <![CDATA[
196 200
197 @MOTHUR_OVERVIEW@ 201 @MOTHUR_OVERVIEW@
198 202
199 **Command Documenation** 203 **Command Documentation**
200 204
201 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. 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.
202 206
203 .. _get.sharedseqs: http://www.mothur.org/wiki/Get.sharedseqs 207 .. _get.sharedseqs: https://www.mothur.org/wiki/Get.sharedseqs
204 208
205 v1.21.0: Updated to Mothur 1.33, added shared file option 209 v1.21.0: Updated to Mothur 1.33, added shared file option
206 ]]> 210 ]]>
207 </help> 211 </help>
208 <expand macro="citations"/> 212 <expand macro="citations"/>