annotate mothur/tools/mothur/read.otu.xml @ 3:b849cd7e132a

workflow cleanup_param_values recurses through paramnames whenever they start with a paramname_, so change input to input_fasta

<tool id="mothur_read_otu" name="Read.otu" version="1.16.0" force_history_refresh="True">
 <description>Read OTU list and group to create a shared file</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='read.otu'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared:'$shared
  --outputdir='$logfile.extra_files_path'
  #if $show_rabund.value == True:
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 
   --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund'
  #end if
  --list=$otu
  --group=$otu_group
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="list" label="list - OTU List"/>
  <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/>
  <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
   <options from_dataset="otu">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>
  <param name="show_rabund" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Put Group rabund files in your history"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="shared" name="shared" label="${tool.name} on ${on_string}: 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 read.otu_ command is called before most of the OTU based mothur commands.  It is included here explicitly to allow the creatation of a shared file from OTU list and group files.  

.. _read.otu: http://www.mothur.org/wiki/Read.otu

 </help>
</tool>