Mercurial > repos > iuc > mothur_count_groups

comparison count.groups.xml @ 1:13a947a26f7a 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 18:08:47 -0400
parents 2d98db6098be
children ed773c45b3d6
comparison
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0:2d98db6098be 1:13a947a26f7a
2 <description>counts the number of sequences represented by a specific group or set of groups</description> 2 <description>counts the number of sequences represented by a specific group or set of 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 "$group" group.dat && 13 ln -s "$group" group.dat &&
11 #if $groupnames.source == "accnos": 14 #if $groupnames.source == "accnos":
12 ln -s "$groupnames.accnos" groupnames.accnos.dat && 15 ln -s "$groupnames.accnos" groupnames.accnos.dat &&
13 #end if 16 #end if
29 ,accnos=groupnames.accnos.dat 32 ,accnos=groupnames.accnos.dat
30 #end if 33 #end if
31 #end if 34 #end if
32 )' 35 )'
33 | sed 's/ //g' ## mothur trips over whitespace 36 | sed 's/ //g' ## mothur trips over whitespace
34 | mothur && 37 | mothur
38 | tee mothur.out.log &&
35 39
36 ## parse relevant tool output from logfile to file 40 ## parse relevant tool output from logfile to file
37 cat mothur.*.logfile 41 cat mothur.*.logfile
38 | head -n-7 42 | head -n-7
39 | sed '1,29d' 43 | sed '1,29d'
78 <help> 82 <help>
79 <![CDATA[ 83 <![CDATA[
80 84
81 @MOTHUR_OVERVIEW@ 85 @MOTHUR_OVERVIEW@
82 86
83 **Command Documenation** 87 **Command Documentation**
84 88
85 The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file. 89 The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file.
86 90
87 .. _shared: http://www.mothur.org/wiki/Shared_file 91 .. _shared: https://www.mothur.org/wiki/Shared_file
88 .. _group: http://www.mothur.org/wiki/Group_file 92 .. _group: https://www.mothur.org/wiki/Group_file
89 .. _count.groups: http://www.mothur.org/wiki/Count.groups 93 .. _count.groups: https://www.mothur.org/wiki/Count.groups
90 ]]> 94 ]]>
91 </help> 95 </help>
92 <expand macro="citations"/> 96 <expand macro="citations"/>
93 </tool> 97 </tool>