annotate mothur/tools/mothur/make.shared.xml @ 36:040410b8167e default tip

Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.

<tool id="mothur_make_shared" name="Make.shared" version="1.23.0" force_history_refresh="True">
 <description>Make a shared file from a list and a group</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='make.shared'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared$:'$shared
  --outputdir='$logfile.extra_files_path'
  #if $as_datasets.__str__ == "yes":
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund'
  #end if
	--list=$list

	#if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('groups').__class__):
		--group=$group
	#else:	
		--count=$group		
	#end if 

  #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 $ordergroup.__str__ != "None" and len($ordergroup.__str__) > 0:
   --ordergroup=$ordergroup
  #end if
  *#
 </command>
 <inputs>
  <param name="list" type="data" format="list" label="list - OTU List"/>
  <param name="group" type="data" format="groups, count" label="group - "/>
  <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" 
     help="By default all are included if no selection is made.">
   <options>
    <filter type="data_meta" ref="list" key="labels" />
   </options>
  </param>
  <param name="groups" type="select" label="groups - Groups to include" multiple="true">
   <options>
    <filter type="data_meta" ref="group" key="groups" />
   </options>
  </param>
  <!--
  <param name="ordergroup" type="data" format="groups" optional="true" label="ordergroup - one column list of group names in desired order"/>
  -->
  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each group rabund"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">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 make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group.


.. _list: http://www.mothur.org/wiki/List_file
.. _group: http://www.mothur.org/wiki/Group_file
.. _shared: http://www.mothur.org/wiki/Shared_file
.. _rabund: http://www.mothur.org/wiki/Rabund_file
.. _make.shared: http://www.mothur.org/wiki/Make.shared

 </help>
</tool>