Mercurial > repos > iuc > mothur_list_seqs

comparison list.seqs.xml @ 1:8fc365d239a2 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 18:31:19 -0400
parents 1fdda3adf67e
children 8fc97e7b351c
comparison
equal deleted inserted replaced
0:1fdda3adf67e 1:8fc365d239a2
2 <description>Lists the names (accnos) of the sequences</description> 2 <description>Lists the names (accnos) of the sequences</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 "$search.input" search.input.dat && 13 ln -s "$search.input" search.input.dat &&
11 14
12 echo 'list.seqs( 15 echo 'list.seqs(
13 #if $search.intype == "fasta": 16 #if $search.intype == "fasta":
28 count=search.input.dat 31 count=search.input.dat
29 #end if 32 #end if
30 )' 33 )'
31 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur 35 | mothur
36 | tee mothur.out.log
33 ]]></command> 37 ]]></command>
34 <inputs> 38 <inputs>
35 <conditional name="search"> 39 <conditional name="search">
36 <param name="intype" type="select" label="Type to list" help=""> 40 <param name="intype" type="select" label="Type to list" help="">
37 <option value="fasta">Sequence Fasta</option> 41 <option value="fasta">Sequence Fasta</option>
90 <help> 94 <help>
91 <![CDATA[ 95 <![CDATA[
92 96
93 @MOTHUR_OVERVIEW@ 97 @MOTHUR_OVERVIEW@
94 98
95 **Command Documenation** 99 **Command Documentation**
96 100
97 The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file. 101 The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file.
98 102
99 .. _name: http://www.mothur.org/wiki/Name_file 103 .. _name: https://www.mothur.org/wiki/Name_file
100 .. _group: http://www.mothur.org/wiki/Group_file 104 .. _group: https://www.mothur.org/wiki/Group_file
101 .. _list: http://www.mothur.org/wiki/List_file 105 .. _list: https://www.mothur.org/wiki/List_file
102 .. _align.report: http://www.mothur.org/wiki/Align.seqs 106 .. _align.report: https://www.mothur.org/wiki/Align.seqs
103 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline 107 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
104 .. _list.seqs: http://www.mothur.org/wiki/list.seqs 108 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
105 109
106 v.1.20.0: Updated to mothur 1.33, added count and fastq option 110 v.1.20.0: Updated to mothur 1.33, added count and fastq option
107 ]]> 111 ]]>
108 </help> 112 </help>
109 <expand macro="citations"/> 113 <expand macro="citations"/>