comparison mothur/tools/mothur/create.database.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

34:1be61ceb20d7

<tool id="mothur_create_database" name="Create.database" version="1.27.0" >
 <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='create.database'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+?\.database$:'$database

  <param name="otu" type="data" format="list,shared" label="list or shared - OTU List of Shared"/>
  <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta"
         help="fasta file output by get.oturep"/>
  <param name="repname" type="data" format="names" label="repname - rep.names"
         help="names file output by get.oturep"/>
  <param name="contaxonomy" type="select" format="cons.taxonomy" label="contaxonomy - Consensus Taxonomy"
         help="consensus taxonomy file output by classify.otu"/>
  <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>

 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

.. _list: http://www.mothur.org/wiki/List_file
.. _shared: http://www.mothur.org/wiki/Shared_file
.. _create.database: http://www.mothur.org/wiki/Create.database


 </help>
</tool>

35:95d75b35e4d2

<tool id="mothur_create_database" name="Create.database" version="1.28.0" >
 <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='create.database'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+?\.database$:'$database

  <param name="otu" type="data" format="list,shared" label="list or shared - OTU List of Shared"/>
  <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta"
         help="fasta file output by get.oturep"/>
  <param name="repname" type="data" format="names" label="repname - rep.names"
         help="names file output by get.oturep"/>
	<param name="count" type="data" format="count_table" label="count file - count_table"/>		 
  <param name="contaxonomy" type="select" format="cons.taxonomy" label="contaxonomy - Consensus Taxonomy"
         help="consensus taxonomy file output by classify.otu"/>
  <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <options>

 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.33">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

.. _list: http://www.mothur.org/wiki/List_file
.. _shared: http://www.mothur.org/wiki/Shared_file
.. _create.database: http://www.mothur.org/wiki/Create.database

v.1.28.0: Updated to Mothur 1.33, added count paramter.


 </help>
</tool>