Mercurial > repos > iuc > mothur_deunique_seqs

comparison deunique.seqs.xml @ 1:623e22d7cb82 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 18:47:48 -0400
parents 57cf9fc6c84a
children 09c8815c455b
comparison
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0:57cf9fc6c84a 1:623e22d7cb82
2 <description>Return all sequences</description> 2 <description>Return all 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 "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 ln -s "$names" names.dat && 14 ln -s "$names" names.dat &&
12 15
13 echo 'deunique.seqs( 16 echo 'deunique.seqs(
18 #end if 21 #end if
19 fasta=fasta.dat 22 fasta=fasta.dat
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="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> 29 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
26 <conditional name="inputtype"> 30 <conditional name="inputtype">
27 <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help=""> 31 <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help="">
72 <help> 76 <help>
73 <![CDATA[ 77 <![CDATA[
74 78
75 @MOTHUR_OVERVIEW@ 79 @MOTHUR_OVERVIEW@
76 80
77 **Command Documenation** 81 **Command Documentation**
78 82
79 The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file. 83 The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.
80 84
81 .. _name: http://www.mothur.org/wiki/Name_file 85 .. _name: https://www.mothur.org/wiki/Name_file
82 .. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs 86 .. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs
83 87
84 v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output 88 v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output
85 89
86 ]]> 90 ]]>
87 </help> 91 </help>