view mothur/tools/mothur/metastats.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

<tool id="mothur_metastats" name="Metastats" version="1.19.0" force_history_refresh="True" >
 <description>generate principle components plot data</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='metastats'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  #if $as_datasets.__str__ == "yes":
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.((unique|[0-9.]*)(\..*?)+\.metastats)$:txt'
  #end if
  --shared=$otu
  --design=$design
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups='$groups'
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  #if 1 >= $threshold >= 0:
   --threshold=$threshold
  #end if
  #if $sets.__str__ != "None" and len($sets.__str__) > 0:
   --sets=$sets
  #end if
  --processors=2
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
    <filter type="unique_value" name="unq_lbl" column="0" />
   </options>
  </param>
  <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="design" type="data" format="tabular" label="design - assign groups to new grouping"
         help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
  <param name="sets" type="select" label="sets - group sets to analyze" multiple="true">
   <options from_dataset="design">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="iters" type="integer" value="1000" label="iters - Number of randomizations (default 1000)"/>
  <param name="threshold" type="float" value="0.05" label="threshold - significance level to reject null hypotheses (ignored if &#060; 0)"/>
  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history datasets for each label"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </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 metastats_ command generate principle components plot data.

.. _metastats: http://www.mothur.org/wiki/Metastats

 </help>
</tool>