Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.rabund.xml @ 15:a6189f58fedb
Mothur - updated for Mothur version 1.22.0
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 08 Nov 2011 11:45:32 -0600 |
parents | e990ac8a0f58 |
children | bfbaf823be4c |
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<tool id="mothur_get_rabund" name="Get.rabund" version="1.19.0"> <description>Get rabund from a otu list or sabund</description> <command interpreter="python"> mothur_wrapper.py --cmd='get.rabund' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rabund$:'$rabund --outputdir='$logfile.extra_files_path' #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): --list=$otu #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): --sabund=$otu #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label=$label #end if $sorted </command> <inputs> <param name="otu" type="data" format="list,sabund" label="list,sabund - List or Sabund"/> <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="sorted" type="boolean" checked="false" truevalue="--sorted=true" falsevalue="" label="sorted - sort by abundance" help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> </outputs> <requirements> <requirement type="binary">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.rabund_ command generates an rabund_ file from a list_ or sabund_ file. .. _rabund: http://www.mothur.org/wiki/Rabund_file .. _list: http://www.mothur.org/wiki/List_file .. _sabund: http://www.mothur.org/wiki/Sabund_file .. _get.rabund: http://www.mothur.org/wiki/Get.rabund </help> </tool>