annotate mothur/tools/mothur/pca.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

<tool id="mothur_pca" name="Pca" version="1.16.0">
 <description>generate principle components plot data</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## 98_sq_phylip_amazon.fn.unique.pca.axes
  ## 98_sq_phylip_amazon.fn.unique.pca.loadings
  --cmd='pca'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pca.axes$:'$pca_axes,'^\S+\.pca.loadings$:'$pca_loadings
  --outputdir='$logfile.extra_files_path'
  --READ_cmd='read.otu'
  #if $input.source == 'similarity':
   --READ_list=$input.otu
   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
    --READ_group='$otu_group'
   #end if
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --READ_groups='$input.groups'
   #end if
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --READ_label='$input.label'
   #end if
  #elif $input.source == 'shared':
   --READ_shared=$input.otu
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --READ_label='$input.label'
   #end if
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --READ_groups='$input.groups'
   #end if
  #end if
  $metric
 </command>
 <inputs>
  <conditional name="input">
   <param name="source" type="select" label="Generate principle components for">
    <option value="similarity">OTU list</option>
    <option value="shared">OTU Shared</option>
   </param>
   <when value="similarity">
     <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
     <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="0"/>
       <column name="value" index="0"/>
      </options>
     </param>
     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
      <options from_dataset="otu_group">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
   </when>
   <when value="shared">
     <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
     <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="0"/>
       <column name="value" index="0"/>
       <filter type="unique_value" name="unq_lbl" column="0" />
      </options>
     </param>
     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
   </when>
  </conditional>
  <param name="metric" type="boolean" truevalue="" falsevalue="--Metric=False" checked="true" label="metric - Calculate pearson correlation coefficient" />
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="axes" name="pca_axes" label="${tool.name} on ${on_string}: pca.axes" />
  <data format="txt" name="pca_loadings" label="${tool.name} on ${on_string}: pca.loadings" />
 </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 pca_ command generate principle components plot data.

.. _pca: http://www.mothur.org/wiki/Pca

 </help>
</tool>