Mercurial > repos > iuc > mothur_split_abund

comparison split.abund.xml @ 1:59ab81a8d28d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:21:32 -0400
parents 2077ddb27f4c
children ef779f6cb288
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0:2077ddb27f4c 1:59ab81a8d28d
2 <description>Separate sequences into rare and abundant groups</description> 2 <description>Separate sequences into rare and abundant groups</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 "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 ln -s "$search.input" search_input.dat && 14 ln -s "$search.input" search_input.dat &&
12 #if $split.dosplit == "yes": 15 #if $split.dosplit == "yes":
13 ln -s "$split.group" split_group.dat && 16 ln -s "$split.group" split_group.dat &&
36 accnos=$accnos, 39 accnos=$accnos,
37 cutoff=$cutoff 40 cutoff=$cutoff
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 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> 47 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
44 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/> 48 <param name="cutoff" type="integer" value="10" min="0" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/>
45 <conditional name="search"> 49 <conditional name="search">
292 <help> 296 <help>
293 <![CDATA[ 297 <![CDATA[
294 298
295 @MOTHUR_OVERVIEW@ 299 @MOTHUR_OVERVIEW@
296 300
297 **Command Documenation** 301 **Command Documentation**
298 302
299 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups. 303 The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups.
300 304
301 .. _list: http://www.mothur.org/wiki/List_file 305 .. _list: https://www.mothur.org/wiki/List_file
302 .. _name: http://www.mothur.org/wiki/Name_file 306 .. _name: https://www.mothur.org/wiki/Name_file
303 .. _split.abund: http://www.mothur.org/wiki/Split.abund 307 .. _split.abund: https://www.mothur.org/wiki/Split.abund
304 ]]> 308 ]]>
305 </help> 309 </help>
306 <expand macro="citations"/> 310 <expand macro="citations"/>
307 </tool> 311 </tool>