Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/deunique.seqs.xml @ 7:7bfe1f843858
Support Mothur v1.20
trim.seqs - added name parameter and optional trim.names output
phylo.diversity - group optional, put group and groups in conditional - breaks
get.lineage remove.lineage - allow multiple taxons
dist.shared - added processors
consensus.seqs - add cutoff parameter
trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs
new tools - chimera.uchime deunique.tree count.seqs
shared/relabund files - Column headings
refactor lib/galaxy/datatypes/metagenomics.py
add filters to label and group selects in tool configs
mothur_wrapper.py updated with new tools params
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 27 Jun 2011 10:12:25 -0500 |
parents | 5265aa9067e0 |
children | 49058b1f8d3f |
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<tool id="mothur_deunique_seqs" name="Deunique.seqs" version="1.20.0"> <description>Return all sequences</description> <command interpreter="python"> mothur_wrapper.py --cmd='deunique.seqs' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.redundant\.fasta$:'$out_fasta --outputdir='$logfile.extra_files_path' --fasta=$fasta --name=$names </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/> <param name="names" type="data" format="names" label="names - Sequences Name reference"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" /> </outputs> <requirements> <requirement type="binary">mothur</requirement> </requirements> <tests> </tests> <help> **Mothur Overview** Mothur_, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan, provides bioinformatics for the microbial ecology community. .. _Mothur: http://www.mothur.org/wiki/Main_Page **Command Documenation** The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file. .. _name: http://www.mothur.org/wiki/Name_file .. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs </help> </tool>