diff mothur/tools/mothur/remove.groups.xml @ 35:95d75b35e4d2

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

--- a/mothur/tools/mothur/remove.groups.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/remove.groups.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_remove_groups" name="Remove.groups" version="1.24.0">
+<tool id="mothur_remove_groups" name="Remove.groups" version="1.25.0">
  <description>Remove groups from groups,fasta,names,list,taxonomy</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -7,8 +7,12 @@
   ## adds .pick before the last extension to the input file
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__]
   --cmd='remove.groups'
-  --outputdir='$logfile.extra_files_path'
-  --group=$group_in
+	--outputdir='$logfile.extra_files_path'
+  #if isinstance($group_in.datatype, $__app__.datatypes_registry.get_datatype_by_extension('group').__class__):
+		--group=$group_in
+	#else
+		--count=$group_in
+	#end if
   #if $groupnames.source == 'groups':
    #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0:
     --groups=$groupnames.groups
@@ -45,7 +49,7 @@
   --result=#echo ','.join($results)
  </command>
  <inputs>
-  <param name="group_in" type="data" format="groups" label="group - Groups"/>
+  <param name="group_in" type="data" format="groups,count_table" label="group - Groups"/>
   <conditional name="groupnames">
    <param name="source" type="select" label="Select Group Names from">
     <option value="groups">A List of Group Names</option>
@@ -94,7 +98,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="package" version="1.27">mothur</requirement>
+  <requirement type="package" version="1.33">mothur</requirement>
  </requirements>
  <tests>
  </tests>