annotate mothur/tools/mothur/get.relabund.xml @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

<tool id="mothur_get_relabund" name="Get.relabund" version="1.20.0">
 <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=$scale
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared" 
    help="Use Make.shared to create a shared file from a list and a group file"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
    <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/>
    <filter type="unique_value" name="unq_lbl" column="0" />
   </options>
  </param>
  <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="scale" type="select" label="scale - Scale by">
   <option value="">Use default</option>
   <option value="totalgroup" selected="true">Total Groups</option>
   <option value="totalotu">Total OTUs</option>
   <option value="averagegroup">Average Groups</option>
   <option value="averageotu">Average OTUs</option>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${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>