Mercurial > repos > iuc > mothur_remove_lineage

comparison remove.lineage.xml @ 1:b4939bc52ca7 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 18:24:59 -0400
parents 152eaafb14ba
children 702f118f52f9
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0:152eaafb14ba 1:b4939bc52ca7
2 <description>Picks by taxon</description> 2 <description>Picks by taxon</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 #import re 12 #import re
10 ## create symlinks to input datasets 13 ## create symlinks to input datasets
11 ln -s "$file.taxonomy" file.taxonomy.dat && 14 ln -s "$file.taxonomy" file.taxonomy.dat &&
12 #if $file.filetype == "useconstaxonomy": 15 #if $file.filetype == "useconstaxonomy":
13 ln -s "$file.shared" file.shared.dat && 16 ln -s "$file.shared" file.shared.dat &&
58 ,count=count.dat 61 ,count=count.dat
59 #end if 62 #end if
60 )' 63 )'
61 | sed 's/ //g' ## mothur trips over whitespace 64 | sed 's/ //g' ## mothur trips over whitespace
62 | mothur 65 | mothur
66 | tee mothur.out.log
63 ]]></command> 67 ]]></command>
64 <inputs> 68 <inputs>
65 <conditional name="file"> 69 <conditional name="file">
66 <param name="filetype" type="select" label="choose which file is used"> 70 <param name="filetype" type="select" label="choose which file is used">
67 <option value="usetaxonomy" selected="true">taxonomy</option> 71 <option value="usetaxonomy" selected="true">taxonomy</option>
189 <help> 193 <help>
190 <![CDATA[ 194 <![CDATA[
191 195
192 @MOTHUR_OVERVIEW@ 196 @MOTHUR_OVERVIEW@
193 197
194 **Command Documenation** 198 **Command Documentation**
195 199
196 The remove.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences. 200 The remove.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences.
197 201
198 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline 202 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
199 .. _name: http://www.mothur.org/wiki/Name_file 203 .. _name: https://www.mothur.org/wiki/Name_file
200 .. _group: http://www.mothur.org/wiki/Group_file 204 .. _group: https://www.mothur.org/wiki/Group_file
201 .. _list: http://www.mothur.org/wiki/List_file 205 .. _list: https://www.mothur.org/wiki/List_file
202 .. _align.report: http://www.mothur.org/wiki/Align.seqs 206 .. _align.report: https://www.mothur.org/wiki/Align.seqs
203 .. _remove.lineage: http://www.mothur.org/wiki/Remove.lineage 207 .. _remove.lineage: https://www.mothur.org/wiki/Remove.lineage
204 208
205 ]]> 209 ]]>
206 </help> 210 </help>
207 <expand macro="citations"/> 211 <expand macro="citations"/>
208 </tool> 212 </tool>