Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/make.shared_from_biom.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 49058b1f8d3f |
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<tool id="mothur_make_shared_from_biom" name="Make.shared " version="1.25.0" force_history_refresh="True"> <description>Make a shared file from a biom file</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path --cmd='make.shared' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared$:'$shared --outputdir='$logfile.extra_files_path' #if $as_datasets.__str__ == "yes": --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' #end if --biom=$biom #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if </command> <inputs> <param name="biom" type="data" format="biom" label="biom - The Biological Observation Matrix"/> <param name="label" type="text" size="40" label="label - to restrict to these OTU Labels" help="multiple labels separated by hyphens, example: unique-0.02-0.04"/> <param name="groups" type="text" size="40" label="groups - restrict to these groups" help="multiple groups separated by hyphens, example: control-group1-group2"/> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each group rabund"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> </outputs> <requirements> <requirement type="package" version="1.27">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.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group. .. _list: http://www.mothur.org/wiki/List_file .. _group: http://www.mothur.org/wiki/Group_file .. _shared: http://www.mothur.org/wiki/Shared_file .. _rabund: http://www.mothur.org/wiki/Rabund_file .. _make.shared: http://www.mothur.org/wiki/Make.shared </help> </tool>