Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.relabund.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
parents | 3202a38e44d9 |
children | e990ac8a0f58 |
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<tool id="mothur_get_relabund" name="Get.relabund" version="1.16.0"> <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' --READ_cmd='read.otu' #if $input.source == 'similarity': --READ_list=$input.otu #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: --READ_group='$otu_group' #end if #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --READ_label='$input.label' #end if #elif $input.source == 'shared': --READ_shared=$input.otu #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: --READ_label='$input.label' #end if #end if #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: --groups=$input.groups #end if #if $scale.__str__ != "None" and len($scale.__str__) > 0: --scale=$scale #end if </command> <inputs> <conditional name="input"> <param name="source" type="select" label="Get Relative abundance for"> <option value="similarity">OTU list</option> <option value="shared">OTU Shared</option> </param> <when value="similarity"> <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> <options from_dataset="otu_group"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> </when> <when value="shared"> <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> <filter type="unique_value" name="unq_lbl" column="0" /> </options> </param> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> <options from_dataset="otu"> <column name="name" index="1"/> <column name="value" index="1"/> <filter type="unique_value" name="unq_grp" column="1" /> </options> </param> </when> </conditional> <param name="scale" type="select" label="scale - Scale by"> <option value="">Use default</option> <option value="totalgroup">Total Groups</option> <option value="totalotu">Total OTUs</option> <option value="averagegroup">Average Groups</option> <option value="averageotu">Average OTUs</option> </param> </inputs> <outputs> <data format="html" name="logfile" label="${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. It outputs a .relabund file. .. _get.relabund: http://www.mothur.org/wiki/Get.relabund </help> </tool>