Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.sabund.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 | 95d75b35e4d2 |
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<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>