annotate mothur/tools/mothur/phylo.diversity.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_phylo_diversity" name="Phylo.diversity" version="1.20.0">
 <description>Alpha Diversity calculates unique branch length</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='phylo.diversity'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.phylodiv\.summary$:'$summary_out,'^\S+\.phylodiv$:'$collectors_out,'^\S+\.rarefaction$:'$rarefaction_out
  --outputdir='$logfile.extra_files_path'
  --tree=$tree
  #if $grouping.use:
   #if $grouping.group.__str__ != "None" and len($grouping.group.__str__) > 0:
    --group='$grouping.group'
   #end if
   #if $grouping.groups.__str__ != "None" and len($grouping.groups.__str__) > 0:
    --groups='$grouping.groups'
   #end if
  #end if
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name='$name'
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  #if float($freq.__str__) > 0:
   --freq=$freq
  #end if
  $scale
  $collect
  $rarefy
  #if len($rarefy.__str__) > 0 or len($collect.__str__) > 0:
   $summary
  #end if
  --processors=2
 </command>
 <inputs>
  <!-- list,group  or shared -->
  <param name="tree" type="data" format="tre" label="tree - Phylogenetic Tree"/>
  <conditional name="grouping">
   <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Analyze by group using a Group file"/>
   <when value="yes">
   <param name="group" type="data" format="groups" label="group - Group file for the tree"/>
   <param name="groups" type="select" label="groups - Groups to display" multiple="true">
    <help>All groups displayed if none are selected.</help>
    <options from_dataset="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="no"/>
  </conditional> <!-- use_groups -->
  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file for the tree"/>
  <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
  <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" 
         help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/>

  <param name="scale" type="boolean" truevalue="--scale=true" falsevalue="" checked="false" label="scale - Scale output to the number of sequences sampled" />
  <param name="rarefy" type="boolean" truevalue="--rarefy=true" falsevalue="" checked="false" label="rarefy - Calculate the rarefaction data" />
  <param name="summary" type="boolean" truevalue="" falsevalue="--summary=false" checked="true" label="summary - Generate a summary file" />
  <param name="collect" type="boolean" truevalue="--collect=true" falsevalue="" checked="false" label="collect - Create a collectors curve" />
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="summary_out" label="${tool.name} on ${on_string}: summary">
   <filter>summary == True</filter>
  </data>
  <data format="tabular" name="rarefaction_out" label="${tool.name} on ${on_string}: rarefaction">
   <filter>rarefy == True</filter>
  </data>
  <data format="tabular" name="collectors_out" label="${tool.name} on ${on_string}: collectors">
   <filter>collect == True</filter>
  </data>
  <!-- random uses input prompts, not sure how to model that
  <data format="tabular" name="random" label="${tool.name} on ${on_string}: random">
  </data>
  -->
 </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 phylo.diversity_ command calculates alpha diversity as the total of the unique branch length. 

.. _phylo.diversity: http://www.mothur.org/wiki/Phylo.diversity


 </help>
</tool>