Mercurial > repos > iuc > mothur_remove_otus

comparison remove.otus.xml @ 1:b6f8dacd95cb 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 18:24:38 -0400
parents 8cef8feb87a7
children a7ee6371e854
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0:8cef8feb87a7 1:b6f8dacd95cb
2 <description>Remove otus containing sequences from specified groups</description> 2 <description>Remove otus containing sequences from specified 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 "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
11 ln -s "$group_in" group_in.dat && 14 ln -s "$group_in" group_in.dat &&
12 15
13 echo 'remove.otus( 16 echo 'remove.otus(
18 ,groups=${ str($groups).replace(",","-") } 21 ,groups=${ str($groups).replace(",","-") }
19 #end if 22 #end if
20 )' 23 )'
21 | sed 's/ //g' ## mothur trips over whitespace 24 | sed 's/ //g' ## mothur trips over whitespace
22 | mothur 25 | mothur
26 | tee mothur.out.log
23 ]]></command> 27 ]]></command>
24 <inputs> 28 <inputs>
25 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 29 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
26 <param name="label" type="select" label="label - OTU Labels" help="Select exactly one label"> 30 <param name="label" type="select" label="label - OTU Labels" help="Select exactly one label">
27 <expand macro="labeloptions"/> 31 <expand macro="labeloptions"/>
52 <help> 56 <help>
53 <![CDATA[ 57 <![CDATA[
54 58
55 @MOTHUR_OVERVIEW@ 59 @MOTHUR_OVERVIEW@
56 60
57 **Command Documenation** 61 **Command Documentation**
58 62
59 The remove.otus_ command removes otus from a list_ containing sequences from a specific group or set of groups. 63 The remove.otus_ command removes otus from a list_ containing sequences from a specific group or set of groups.
60 64
61 .. _list: http://www.mothur.org/wiki/List_file 65 .. _list: https://www.mothur.org/wiki/List_file
62 .. _remove.otus: http://www.mothur.org/wiki/Remove.otus 66 .. _remove.otus: https://www.mothur.org/wiki/Remove.otus
63 67
64 ]]> 68 ]]>
65 </help> 69 </help>
66 <expand macro="citations"/> 70 <expand macro="citations"/>
67 </tool> 71 </tool>