annotate mothur/tools/mothur/get.otus.xml @ 2:e990ac8a0f58

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

<tool id="mothur_get_otus" name="Get.otus" version="1.19.0">
 <description>Get otus containing sequences from specified groups</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='get.otus'
  --outputdir='$logfile.extra_files_path'
  --group=$group_in
  --list=$list_in
  --label=$label
  #if $groupnames.source == 'groups':
   #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0:
    --groups=$groupnames.groups
   #end if
  #else
   #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0:
    --accnos=$groupnames.accnos
   #end if
  #end if
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  #set results = $results + ["'" + $re.sub(r'^(.*)\.(.*?)',r'\1.pick.' + $label.__str__ + r'.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__]
  #set results = $results + ["'" + $re.sub(r'^(.*)\.(.*?)',r'\1.pick.'+ $label.__str__ + r'.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__]
  --result=#echo ','.join($results)
 </command>
 <inputs>
  <param name="group_in" type="data" format="groups" label="group - Groups"/>
  <param name="list_in" type="data" format="list" label="list - OTU List"/>
  <param name="label" type="select" label="label - OTU Labels" >
   <options from_dataset="list_in">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>
  <conditional name="groupnames">
   <param name="source" type="select" label="Select Group Names from">
    <option value="groups">A List of Group Names</option>
    <option value="accnos">A History Group Name Accnos Dataset</option>
   </param>
   <when value="groups">
    <param name="groups" type="select" label="groups - Pick groups to include" multiple="true"  force_select="true">
     <help>At least one group must be selected</help>
     <options from_dataset="group_in">
      <column name="name" index="1"/>
      <column name="value" index="1"/>
      <filter type="unique_value" name="unq_grp" column="1" />
     </options>
    </param>
   </when>
   <when value="accnos">
    <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Group Names from your history"/>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/>
  <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/>
 </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 get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups.

.. _list: http://www.mothur.org/wiki/List_file
.. _get.otus: http://www.mothur.org/wiki/Get.otus


 </help>
</tool>