annotate mothur/tools/mothur/normalize.shared.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_normalize_shared" name="Normalize.shared" version="1.20.0">
 <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=$norm
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU Shared or Relabund file"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
    <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/>
    <filter type="unique_value" name="unq_lbl" column="0" />
   </options>
  </param>
  <param name="groups" type="select" label="groups - Groups to include" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="norm" type="integer" value="0" label="norm - Number to normalize to (Uses default if &lt; 1)"
         help="By default this is set to the number of sequences in your smallest group."/>
  <param name="method" type="select" optional="true" label="method - Normalization method">
   <option value="">Use Default</option>
   <option value="totalgroup" selected="true">Total Group</option>
   <option value="zscore">Z Score</option>
  </param>
  <param name="makerelabund" type="boolean" truevalue="--makerelabund=true" falsevalue="" checked="false" label="makerelabund - convert a shared file to a relabund file before you normalize" />
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="shared" name="shared" label="${tool.name} on ${on_string}: norm.shared" />
 </outputs>
 <requirements>
  <requirement type="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 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>