Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/normalize.shared.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_normalize_shared" name="Normalize.shared" version="1.21.0"> <description>Normalize the number of sequences per group to a specified level</description> <command interpreter="python"> mothur_wrapper.py --cmd='normalize.shared' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.norm\.shared$:'$shared --outputdir='$logfile.extra_files_path' #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$otu $makerelabund #elif isinstance($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=$method #end if #if int($norm.__str__) > 0: --norm=$norm #end if </command> <inputs> <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options> <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="groups" type="select" label="groups - Groups to include" multiple="true"> <options> <filter type="data_meta" ref="otu" key="groups" /> </options> </param> <param name="norm" type="integer" value="0" label="norm - Number to normalize to (Uses default if < 1)" help="By default this is set to the number of sequences in your smallest group."/> <param name="method" type="select" optional="true" label="method - Normalization method"> <option value="">Use Default</option> <option value="totalgroup" selected="true">Total Group</option> <option value="zscore">Z Score</option> </param> <param name="makerelabund" type="boolean" truevalue="--makerelabund=true" falsevalue="" checked="false" label="makerelabund - convert a shared file to a relabund file before you normalize" /> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="shared" name="shared" label="${tool.name} on ${on_string}: norm.shared" /> </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 normalize.shared_ command normalizes the number of sequences per group to a specified level. The input is a shared_ or relabund_ file. .. _shared: http://www.mothur.org/wiki/Shared_file .. _relabund: http://www.mothur.org/wiki/Get.relabund .. _normalize.shared: http://www.mothur.org/wiki/Normalize.shared </help> </tool>