Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/bin.seqs.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 5265aa9067e0 |
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<tool id="mothur_bin_seqs" name="Bin.seqs" version="1.19.0" force_history_refresh="True"> <description>Order Sequences by OTU</description> <command interpreter="python"> mothur_wrapper.py --cmd='bin.seqs' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:fasta' --fasta=$fasta --list=$otu #if $name.__str__ != "None" and len($name.__str__) > 0: --name=$name #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if $group.__str__ != "None" and len($group.__str__) > 0: --group='$group' #end if </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/> <param name="otu" type="data" format="list" label="list - OTU List"/> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </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 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. .. _list_file: http://www.mothur.org/wiki/List_file .. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs </help> </tool>