Mercurial > repos > iuc > mothur_split_groups

comparison split.groups.xml @ 1:87bee516388b 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 04:35:10 -0400
parents 089c0f0c6c18
children 883a95e17395
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0:089c0f0c6c18 1:87bee516388b
2 <description>Generates a fasta file for each group</description> 2 <description>Generates a fasta file for each 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 "$name" name.dat && 13 ln -s "$name" name.dat &&
11 ln -s "$count" count.dat && 14 ln -s "$count" count.dat &&
12 ln -s "$fasta" fasta.dat && 15 ln -s "$fasta" fasta.dat &&
13 ln -s "$group" group.dat && 16 ln -s "$group" group.dat &&
25 fasta=fasta.dat, 28 fasta=fasta.dat,
26 group=group.dat 29 group=group.dat
27 )' 30 )'
28 | sed 's/ //g' ## mothur trips over whitespace 31 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur 32 | mothur
33 | tee mothur.out.log
30 ]]></command> 34 ]]></command>
31 <inputs> 35 <inputs>
32 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/> 36 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
33 <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/> 37 <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
34 <param name="group" type="data" format="mothur.groups" label="group - Groups"/> 38 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
60 <help> 64 <help>
61 <![CDATA[ 65 <![CDATA[
62 66
63 @MOTHUR_OVERVIEW@ 67 @MOTHUR_OVERVIEW@
64 68
65 **Command Documenation** 69 **Command Documentation**
66 70
67 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups. 71 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups.
68 72
69 .. _group: http://www.mothur.org/wiki/Group_file 73 .. _group: https://www.mothur.org/wiki/Group_file
70 .. _name: http://www.mothur.org/wiki/Name_file 74 .. _name: https://www.mothur.org/wiki/Name_file
71 .. _split.groups: http://www.mothur.org/wiki/Split.groups 75 .. _split.groups: https://www.mothur.org/wiki/Split.groups
72 ]]> 76 ]]>
73 </help> 77 </help>
74 <expand macro="citations"/> 78 <expand macro="citations"/>
75 </tool> 79 </tool>