diff mothur/tools/mothur/get.group.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/get.group.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/get.group.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,54 +1,14 @@
-<tool id="mothur_get_group" name="Get.group" version="1.16.0">
+<tool id="mothur_get_group" name="Get.group" version="1.19.0">
  <description>group names from shared or from list and group</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='get.group'
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.bootGroups$:'$bootgroups
   --outputdir='$logfile.extra_files_path'
-  --READ_cmd='read.otu'
-  #if $input.source == 'similarity':
-   --READ_list=$input.otu
-   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
-    --READ_group='$otu_group'
-   #end if
-   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-    --READ_groups='$input.groups'
-   #end if
-  #elif $input.source == 'shared':
-   --READ_shared=$input.otu
-   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
-    --READ_group='$otu_group'
-   #end if
-  #end if
+  --shared=$otu
  </command>
  <inputs>
-  <conditional name="input">
-   <param name="source" type="select" label="Generate principle components for">
-    <option value="similarity">OTU list</option>
-    <option value="shared">OTU Shared</option>
-   </param>
-   <when value="similarity">
-     <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
-     <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/>
-     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
-      <options from_dataset="otu_group">
-       <column name="name" index="1"/>
-       <column name="value" index="1"/>
-       <filter type="unique_value" name="unq_grp" column="1" />
-      </options>
-     </param>
-   </when>
-   <when value="shared">
-     <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
-     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
-      <options from_dataset="otu">
-       <column name="name" index="1"/>
-       <column name="value" index="1"/>
-       <filter type="unique_value" name="unq_grp" column="1" />
-      </options>
-     </param>
-   </when>
-  </conditional>
+  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />