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annotate mothur/tools/mothur/deunique.seqs.xml @ 8:3249eb52a9c1

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trim.seqs name parameter needs to be optional
author Jim Johnson <jj@umn.edu>
date Tue, 05 Jul 2011 13:07:40 -0500
parents 7bfe1f843858
children 49058b1f8d3f
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7bfe1f843858 Support Mothur v1.20
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1 <tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.20.0">
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2 <description>Return all sequences</description>
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3 <command interpreter="python">
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4 mothur_wrapper.py
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5 --cmd='deunique.seqs'
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.redundant\.fasta$:'$out_fasta
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7 --outputdir='$logfile.extra_files_path'
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8 --fasta=$fasta
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9 --name=$names
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10 </command>
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11 <inputs>
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12 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
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13 <param name="names" type="data" format="names" label="names - Sequences Name reference"/>
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14 </inputs>
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15 <outputs>
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16 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
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5265aa9067e0 set output formats to match input formats
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17 <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
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18 </outputs>
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19 <requirements>
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20 <requirement type="binary">mothur</requirement>
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21 </requirements>
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22 <tests>
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23 </tests>
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24 <help>
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25 **Mothur Overview**
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26
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27 Mothur_, initiated by Dr. Patrick Schloss and his software development team
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28 in the Department of Microbiology and Immunology at The University of Michigan,
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29 provides bioinformatics for the microbial ecology community.
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30
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31 .. _Mothur: http://www.mothur.org/wiki/Main_Page
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32
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33 **Command Documenation**
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34
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35 The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.
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37 .. _name: http://www.mothur.org/wiki/Name_file
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38 .. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs
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40
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41 </help>
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42 </tool>