Mercurial > repos > iuc > mothur_parse_list

comparison parse.list.xml @ 1:033b821e30e1 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 18:18:19 -0400
parents 0817dd05dbaf
children fe05fc98c62a
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0:0817dd05dbaf 1:033b821e30e1
2 <description>Generate a List file for each group</description> 2 <description>Generate a List 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 "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
11 ln -s "$group" group.dat && 14 ln -s "$group" group.dat &&
12 ln -s "$count" count.dat && 15 ln -s "$count" count.dat &&
13 16
21 #end if 24 #end if
22 group=group.dat 25 group=group.dat
23 )' 26 )'
24 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur 28 | mothur
29 | tee mothur.out.log
26 ]]></command> 30 ]]></command>
27 <inputs> 31 <inputs>
28 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 32 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
29 <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/> 33 <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/>
30 <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include"> 34 <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include">
58 <help> 62 <help>
59 <![CDATA[ 63 <![CDATA[
60 64
61 @MOTHUR_OVERVIEW@ 65 @MOTHUR_OVERVIEW@
62 66
63 **Command Documenation** 67 **Command Documentation**
64 68
65 The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile. 69 The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile.
66 70
67 .. _list: http://www.mothur.org/wiki/List_file 71 .. _list: https://www.mothur.org/wiki/List_file
68 .. _group: http://www.mothur.org/wiki/Group_file 72 .. _group: https://www.mothur.org/wiki/Group_file
69 .. _parse.list: http://www.mothur.org/wiki/Parse.list 73 .. _parse.list: https://www.mothur.org/wiki/Parse.list
70 74
71 v.1.19.0: Updated to mothur 1.33, added count parameter 75 v.1.19.0: Updated to mothur 1.33, added count parameter
72 ]]> 76 ]]>
73 </help> 77 </help>
74 <expand macro="citations"/> 78 <expand macro="citations"/>