diff mothur/tools/mothur/create.database.xml @ 7:3cfe41810949 draft

Update to mothur v 1.27

--- a/mothur/tools/mothur/create.database.xml	Tue Nov 27 09:04:17 2012 -0600
+++ b/mothur/tools/mothur/create.database.xml	Fri Nov 30 08:16:51 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_create_database" name="Create.database" version="1.25.0" >
+<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 
@@ -7,7 +7,11 @@
   --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
+  #if isinstance($group.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
+    --shared=$otu
+  #else
+    --list=$otu
+  #end if
   --repfasta=$repfasta
   --repname=$repname
   --contaxonomy=$contaxonomy
@@ -19,7 +23,7 @@
   #end if
  </command>
  <inputs>
-  <param name="otu" type="data" format="list" label="list - OTU List "/>
+  <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"
@@ -38,7 +42,7 @@
   <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" />
  </outputs>
  <requirements>
-  <requirement type="package" version="1.24.1">mothur</requirement>
+  <requirement type="package" version="1.27">mothur</requirement>
  </requirements>
  <tests>
  </tests>
@@ -53,9 +57,10 @@
 
 **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. 
+The create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file. 
 
 .. _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