diff mothur/tools/mothur/create.database.xml @ 26:5c77423823cb

Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/create.database.xml	Wed May 16 13:12:05 2012 -0500
@@ -0,0 +1,63 @@
+<tool id="mothur_create_database" name="Create.database" version="1.25.0" >
+ <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
+  --outputdir='$logfile.extra_files_path'
+  ## --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+  ## --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary'
+  --list=$otu
+  --repfasta=$repfasta
+  --repname=$repname
+  --contaxonomy=$contaxonomy
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label='$label'
+  #end if
+  #if $group.__str__ != "None" and len($group.__str__) > 0:
+   --group='$group'
+  #end if
+ </command>
+ <inputs>
+  <param name="otu" type="data" format="list" label="list - OTU List "/>
+  <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta"
+         help="fasta file output by get.oturep"/>
+  <param name="repname" type="data" format="names" label="repname - rep.names"
+         help="names file output by get.oturep"/>
+  <param name="contaxonomy" type="select" format="cons.taxonomy" label="contaxonomy - Consensus Taxonomy"
+         help="consensus taxonomy file output by classify.otu"/>
+  <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/>
+  <param name="label" type="select" label="label - OTU Labels" multiple="true">
+   <options>
+    <filter type="data_meta" ref="otu" key="labels" />
+   </options>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" />
+ </outputs>
+ <requirements>
+  <requirement type="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 create.database_ command reads a list_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file. 
+
+.. _list: http://www.mothur.org/wiki/List_file
+.. _create.database: http://www.mothur.org/wiki/Create.database
+
+
+ </help>
+</tool>