view mothur/tools/mothur/bin.seqs.xml @ 36:040410b8167e default tip

Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.

<tool id="mothur_bin_seqs" name="Bin.seqs" version="1.21.0" 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='$__new_file_path__' 
			--new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}'
			--fasta=$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
		#if $count.__str__ != "None" and len($count.__str__) > 0:
			--count='$count'
		#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>
				<filter type="data_meta" ref="otu" key="labels" />
			</options>
		</param>
		<param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
		<param name="count" type="data" format="count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/>
	</inputs>
	<outputs>
		<data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
	</outputs>
	<requirements>
		<requirement type="package" version="1.33">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>