diff mothur/tools/mothur/get.groups.xml @ 24:09740be2bc9c

Mothur - updates for Mothur version 1.24

--- a/mothur/tools/mothur/get.groups.xml	Thu Jan 19 11:27:37 2012 -0600
+++ b/mothur/tools/mothur/get.groups.xml	Wed Mar 28 15:45:03 2012 -0500
@@ -1,4 +1,4 @@
-<tool id="mothur_get_groups" name="Get.groups" version="1.21.0">
+<tool id="mothur_get_groups" name="Get.groups" version="1.24.0">
  <description>Select groups</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -38,6 +38,10 @@
    --taxonomy=$taxonomy_in
    #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__]
   #end if
+  #if $design_in.__str__ != "None" and len($design_in.__str__) > 0:
+   --design=$design_in
+   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($design_in.__str__)) + ":'" + $design_out.__str__]
+  #end if
   --result=#echo ','.join($results)
  </command>
  <inputs>
@@ -65,6 +69,8 @@
   <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
   <param name="shared_in" type="data" format="shared" optional="true" label="shared - OTU Shared"/>
   <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
+  <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping"
+         help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -85,6 +91,9 @@
   <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
    <filter>taxonomy_in != None</filter>
   </data>
+  <data format="design" name="design_out" label="${tool.name} on ${on_string}: pick.design">
+   <filter>design_in != None</filter>
+  </data>
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>