Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/otu.association.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
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<tool id="mothur_otu_association" name="Otu.association" version="1.25.0" force_history_refresh="True"> <description>Calculate the correlation coefficient for the otus</description> <command interpreter="python"> mothur_wrapper.py --cmd='otu.association' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.norm\.shared$:'$shared --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.otu.corr$:$tabular' #if isinstance($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 #if $method.__str__ != "None" and len($method.__str__) > 0: --method=$method #end if #if $metadata.__str__ != "None" and len($method.__str__) > 0: --metadata=$metadata #end if #if $cutoff.__str__ != '': --cutoff=$cutoff #end if </command> <inputs> <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> <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 - Groups to include" multiple="true"> <options> <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="method" type="select" label="method - Normalization method"> <option value="pearson" selected="true">pearson</option> <option value="spearman">spearman</option> <option value="kendall">kendall</option> </param> <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/> <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/> </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 otu.association_ command calculates the correlation coefficient for the otus in a shared_ or relabund_ file. .. _shared: http://www.mothur.org/wiki/Shared_file .. _relabund: http://www.mothur.org/wiki/Get.relabund .. _otu.association: http://www.mothur.org/wiki/Otu.association v.1.25.0: Updated to mothur 1.33, added cutoff option </help> </tool>