view mothur/tools/mothur/count.groups.xml @ 27:49058b1f8d3f

Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur

<tool id="mothur_count_groups" name="Count.groups" version="1.22.0" >
 <description>counts the number of sequences represented by a specific group or set of groups</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='count.groups'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.groups.count$:'$grp_count
  --outputdir='$logfile.extra_files_path'
  #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$group
  #elif isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('count_table').__class__):
   --count=$group
  #else:
   --group=$group
  #end if
  #if $groupnames.source == 'groups':
   #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0:
    --groups=$groupnames.groups
   #end if
  #elif $groupnames.source == 'accnos':
   #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0:
    --accnos=$groupnames.accnos
   #end if
  #end if
 </command>
 <inputs>
  <param name="group" type="data" format="groups,shared,count_table" label="group, shared, or count_table - Group file for sequence count"/>
  <conditional name="groupnames">
   <param name="source" type="select" label="Filter group names">
    <option value="none">Report on All Groups</option>
    <option value="groups">A List of Group Names</option>
    <option value="accnos">A History Group Name Accnos Dataset</option>
   </param>
   <when value="none"/>
   <when value="groups">
    <param name="groups" type="select" label="groups - Pick groups to include" multiple="true">
     <help>All groups displayed if none are selected.</help>
     <options>
      <filter type="data_meta" ref="group" key="groups" />
     </options>
    </param>
   </when>
   <when value="accnos">
    <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Group Names from your history"/>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="grp_count" label="${tool.name} on ${on_string}: group.count" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">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 count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file.

.. _shared: http://www.mothur.org/wiki/Shared_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _count.groups: http://www.mothur.org/wiki/Count.groups

 </help>
</tool>