annotate mothur/tools/mothur/indicator.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_indicator" name="Indicator" version="1.20.0">
 <description>Identify indicator "species" for nodes on a tree</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## output {group_file_name}.pick.{label}.groups   {list_file_name}.pick.{label}.list 
  #import re, os.path
  --cmd='indicator'
  --outputdir='$logfile.extra_files_path'
  --tree=$tree
  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$otu
  #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 $design.__str__ != "None" and len($design.__str__) > 0:
   --design=$design
  #end if
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.indicator.tre$:'$tree_out,'^\S+\.indicator.summary$:'$summary
 </command>
 <inputs>
  <param name="tree" type="data" format="tree" label="tree - A newick-formatted tree"/>
  <param name="otu" type="data" format="shared,relabund" label="shared/relabund - Otu dataset"/>
  <param name="label" type="select" optional="true" label="label - OTU Labels" >
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
    <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/>
    <filter type="unique_value" name="unq_lbl" column="0" />
   </options>
  </param>
  <param name="groups" type="select" optional="true" label="groups - Pick groups to annalyze" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="design" type="data" format="tabular" optional="true" label="design - assign groups to new grouping"
         help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tre" name="tree_out" label="${tool.name} on ${on_string}: indicator.tre"/>
  <data format="txt" name="summary" label="${tool.name} on ${on_string}: indicator.summary"/>
 </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 indicator_ command reads a shared_ or relabund file and a tree file, and outputs a .indicator.tre and .indicator.summary file. The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file. The summary file lists the indicator value for each OTU for each node.

.. _shared: http://www.mothur.org/wiki/Shared_file
.. _indicator: http://www.mothur.org/wiki/Indicator


 </help>
</tool>