annotate mothur/tools/mothur/get.sabund.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

<tool id="mothur_get_sabund" name="Get.sabund" version="1.20.0">
	<description>Get sabund from a otu list or rabund</description>
	<command interpreter="python">
		mothur_wrapper.py 
		--cmd='get.sabund'
		--result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund
		--outputdir='$logfile.extra_files_path'
		#if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
		--list=$otu
		#elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
		--rabund=$otu
		#end if
		#if $label.__str__ != "None" and len($label.__str__) > 0:
		--label=$label
		#end if
		#if $count.__str__ != "None" and len($count.__str__) > 0:
		--count=$count
		#end if
	</command>
	<inputs>
		<param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/>
		<param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
			<options>
				<filter type="data_meta" ref="otu" key="labels" />
			</options>
		</param>
		<param name = "count" type="data" format="count_table" optional="true" help ="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/>

	</inputs>
	<outputs>
		<data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
		<data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
	</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 get.sabund_ command generates an sabund_ file from a list_ or rabund_ file.

		.. _sabund: http://www.mothur.org/wiki/Sabund_file
		.. _list: http://www.mothur.org/wiki/List_file
		.. _rabund: http://www.mothur.org/wiki/Rabund_file
		.. _get.sabund: http://www.mothur.org/wiki/Get.sabund


	</help>
</tool>