Mercurial > repos > iuc > mothur_sort_seqs

comparison sort.seqs.xml @ 1:9900cd702dcf 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 18:10:17 -0400
parents 60c599375cad
children af77b7eda3ce
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0:60c599375cad 1:9900cd702dcf
2 <description>put sequences in different files in the same order</description> 2 <description>put sequences in different files in the same order</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 "$fasta_in" fasta_in.dat && 13 ln -s "$fasta_in" fasta_in.dat &&
11 ln -s "$qfile_in" qfile_in.dat && 14 ln -s "$qfile_in" qfile_in.dat &&
12 ln -s "$flow_in" flow_in.dat && 15 ln -s "$flow_in" flow_in.dat &&
13 ln -s "$name_in" name_in.dat && 16 ln -s "$name_in" name_in.dat &&
43 #end if 46 #end if
44 large=$large 47 large=$large
45 )' 48 )'
46 | sed 's/ //g' ## mothur trips over whitespace 49 | sed 's/ //g' ## mothur trips over whitespace
47 | mothur 50 | mothur
51 | tee mothur.out.log
48 ]]></command> 52 ]]></command>
49 <inputs> 53 <inputs>
50 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/> 54 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/>
51 <param name="qfile_in" type="data" format="qual454" optional="true" label="qfile - sequence quality" help="format must be qual454"/> 55 <param name="qfile_in" type="data" format="qual454" optional="true" label="qfile - sequence quality" help="format must be qual454"/>
52 <param name="flow_in" type="data" format="mothur.sff.flow" optional="true" label="flow - sff flowgram" help="format must be mothur.sff.flow"/> 56 <param name="flow_in" type="data" format="mothur.sff.flow" optional="true" label="flow - sff flowgram" help="format must be mothur.sff.flow"/>
113 <help> 117 <help>
114 <![CDATA[ 118 <![CDATA[
115 119
116 @MOTHUR_OVERVIEW@ 120 @MOTHUR_OVERVIEW@
117 121
118 **Command Documenation** 122 **Command Documentation**
119 123
120 The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order. 124 The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order.
121 You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads. 125 You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.
122 126
123 .. _sort.seqs: http://www.mothur.org/wiki/Sort.seqs 127 .. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs
124 128
125 ]]> 129 ]]>
126 </help> 130 </help>
127 <expand macro="citations"/> 131 <expand macro="citations"/>
128 </tool> 132 </tool>