Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/list.otulabels.xml @ 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Tue, 04 Dec 2012 11:05:19 -0600 |
parents | |
children | 95d75b35e4d2 |
line wrap: on
line source
<tool id="mothur_list_otulabels" name="List.otulabels" version="1.26.0"> <description>Lists otu labels from shared or relabund file</description> <command interpreter="python"> mothur_wrapper.py --cmd='list.otulabels' --outputdir='$logfile.extra_files_path' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.otulabels$:'$otulabels #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$otu #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__): --relabund=$otu #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=$groups #end if </command> <inputs> <param name="otu" type="data" format="shared,relabund" label="shared or relabund - OTU Shared or Relabund"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options> <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true"> <options> <filter type="data_meta" ref="otu" key="groups" /> </options> </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="otulabels" name="otulabels" label="${tool.name} on ${on_string}: otulabels"/> </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 list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otulabels_ or remove.otulabels_ commands. .. _list.otulabels: http://www.mothur.org/wiki/List.otulabels .. _classify.otu: http://www.mothur.org/wiki/Classify.otu .. _otu.association: http://www.mothur.org/wiki/Otu.association .. _corr.axes: http://www.mothur.org/wiki/Corr.axes .. _get.otulabels: http://www.mothur.org/wiki/Get.otulabels .. _remove.otulabels: http://www.mothur.org/wiki/Remove.otulabels .. _shared: http://www.mothur.org/wiki/Shared_file .. _relabund: http://www.mothur.org/wiki/Get.relabund </help> </tool>