Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.relabund.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 7bfe1f843858 |
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<tool id="mothur_get_relabund" name="Get.relabund" version="1.19.0"> <description>Calculate the relative abundance of each otu</description> <command interpreter="python"> mothur_wrapper.py --cmd='get.relabund' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.relabund$:'$relabund --outputdir='$logfile.extra_files_path' --shared=$otu #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 $scale.__str__ != "None" and len($scale.__str__) > 0: --scale=$scale #end if </command> <inputs> <param name="otu" type="data" format="shared" label="shared - OTU Shared" help="Use Make.shared to create a shared file from a list and a group file"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="unique_value" name="unq_lbl" column="0" /> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> <options from_dataset="otu"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> <param name="scale" type="select" label="scale - Scale by"> <option value="">Use default</option> <option value="totalgroup" selected="true">Total Groups</option> <option value="totalotu">Total OTUs</option> <option value="averagegroup">Average Groups</option> <option value="averageotu">Average OTUs</option> </param> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="relabund" name="relabund" label="${tool.name} on ${on_string}: relabund" /> </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.relabund_ command calculates the relative abundance of each otu in a sample from a shared_ file. It outputs a .relabund_ file. .. _shared: http://www.mothur.org/wiki/Shared_file .. _get.relabund: http://www.mothur.org/wiki/Get.relabund </help> </tool>