Mercurial > repos > iuc > mothur_bin_seqs

comparison bin.seqs.xml @ 1:c6461f53ded3 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 18:46:58 -0400
parents c9045fb0bf49
children cb91c12c8a34
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0:c9045fb0bf49 1:c6461f53ded3
2 <description>Order Sequences by OTU</description> 2 <description>Order Sequences by OTU</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 "$group" group.dat && 14 ln -s "$group" group.dat &&
12 ln -s "$fasta" fasta.dat && 15 ln -s "$fasta" fasta.dat &&
13 ln -s "$otu" otu.dat && 16 ln -s "$otu" otu.dat &&
29 fasta=fasta.dat, 32 fasta=fasta.dat,
30 list=otu.dat 33 list=otu.dat
31 )' 34 )'
32 | sed 's/ //g' ## mothur trips over whitespace 35 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur 36 | mothur
37 | tee mothur.out.log
34 ]]></command> 38 ]]></command>
35 <inputs> 39 <inputs>
36 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/> 40 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
37 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 41 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
38 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> 42 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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 bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences. 83 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.
80 84
81 .. _list_file: http://www.mothur.org/wiki/List_file 85 .. _list_file: https://www.mothur.org/wiki/List_file
82 .. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs 86 .. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs
83 ]]> 87 ]]>
84 </help> 88 </help>
85 <expand macro="citations"/> 89 <expand macro="citations"/>
86 </tool> 90 </tool>