view mothur/tools/mothur/cluster.fragments.xml @ 36:040410b8167e default tip

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

<tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.21.0">
	<description> Group sequences that are part of a larger sequence</description>
	<command interpreter="python">
		mothur_wrapper.py 
		--cmd='cluster.fragments'
		--result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fragclust\.\w+$:'$out_fasta,'^\S+\.names$:'$out_names
		--outputdir='$logfile.extra_files_path'
		--fasta=$fasta
		--name=$names
		#if int($diffs.__str__) > 0:
		--diffs=$diffs
		#end if
		#if 100 >= int($percent.__str__) > 0:
		--percent=$percent
		#end if
#if $count.__str__ != "None" and len($count.__str__) > 0:
	--count=$count
#end if
	</command>
	<inputs>
		<param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
		<param name="names" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
		<param name="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)"/>
		<param name="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" 
			help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge.">
			<validator type="in_range" message="percentage differences allowed  must be between 0 and 100" min="0" max="100"/>
		</param>
<param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
	</inputs>
	<outputs>
		<data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
		<data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
		<data format="names" name="out_names" label="${tool.name} on ${on_string}: names" />
	</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 cluster.fragments_ command groups sequences that are part of a larger sequence.

		.. _cluster.fragments: http://www.mothur.org/wiki/Cluster.fragments

		v1.21: Updated to Mothur 1.33. Added count parameter.


	</help>
</tool>