Mercurial > repos > jjohnson > mothur_toolsuite

<tool id="mothur_make_biom" name="Make.biom" version="1.26.0" force_history_refresh="True">
	<description>Make biom files from a shared file</description>
	<command interpreter="python">
		mothur_wrapper.py
		#import re, os.path
		--cmd='make.biom'
		--result='^mothur.\S+\.logfile$:'$logfile
		--outputdir='$logfile.extra_files_path'
		--datasetid='$logfile.id' --new_file_path='$__new_file_path__'
		--new_datasets='^\S+?\.((\S+)\.biom)$:biom'
		--shared=$shared
		#if $contaxonomy.__str__ != 'None' and len($contaxonomy.__str__) > 0:
			--constaxonomy=$contaxonomy
		#end if
		#if $label.__str__ != "None" and len($label.__str__) > 0:
			--label='$label'
		#end if
		#if $groups.__str__ != "None" and len($groups.__str__) > 0:
			--groups=$groups
		#end if
		--matrixtype=$matrixtype
		#if $metadata.__str__ != 'None' and len($metadata.__str__) > 0:
			--metadata=$metadata
		#end if
		#if $picrustc.use:
			#if $picrustc.picrust.__str__ != '':
				--picrust=$picrustc.picrust
			#end if
			#if $picrustc.reftax.__str__ != '':
				--reftaxonomy=$picrustc.reftax
			#end if
		#end if
	</command>
	<inputs>
		<param name="shared" type="data" format="shared" label="shared - OTU Shared file"/>
		<param name="contaxonomy" type="data" format="cons.taxonomy" label="contaxonomy - consensus taxonomy"
			help="The contaxonomy file is the taxonomy file outputted by classify.otu"
			optional="true"
			/>
		<param name = "metadata" type = "data" format = "metadata" label = "metadata" optional="true" help="You can add sample data support here."/>
		<conditional name = "picrustc">
			<param name = "use" type = "boolean" truevalue = "yes" falsevalue = "no" checked="false" label = "use picrust program"/>
			<when value = "yes">
				<param name = "picrust" type = "data" format ="otu_map" label = "picrust" help="The picrust program requires green genes OTU IDs. The picrust parameter allows you to provide the OTU ID mapping table associated with your reference taxonomy."/>
				<param name = "reftax" type = "data" format = "tax" label = "reftaxonomy" help="The referencetax parameter is used with the picrust parameter. Picrust requires the greengenes OTU IDs to be in the biom file, and the referencetax parameter allows you to provide your reference taxonomy file you used when classifying your sequences."/>
			</when>
			<when value = "no"/>
		</conditional>

		<param name="matrixtype" type="select" label="matrixtype - sparse or dense">
			<option value="sparse">sparse</option>
			<option value="dense">dense</option>
		</param>
		<param name="groups" type="select" label="groups - Groups to include" multiple="true"
			help="By default all are included if no selection is made.">
			<options>
				<filter type="data_meta" ref="shared" key="groups" />
			</options>
		</param>
		<param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true"
			help="By default all are included if no selection is made.">
			<options>
				<filter type="data_meta" ref="shared" key="labels" />
			</options>
		</param>
	</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 make.biom command converts a shared_ shared file to biom_ files.
		The output can be filtered by groups and labels.


		.. _shared: http://www.mothur.org/wiki/Shared_file
		.. _biom:  http://biom-format.org/documentation/biom_format.html
		.. _make.biom: http://www.mothur.org/wiki/Make.biom

	</help>
</tool>
author	certain cat
date	Fri, 31 Oct 2014 15:09:32 -0400
parents	49058b1f8d3f
children