diff mothur/tools/mothur/get.group.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/get.group.xml	Tue Jun 07 17:35:35 2011 -0400
@@ -0,0 +1,78 @@
+<tool id="mothur_get_group" name="Get.group" version="1.16.0">
+ <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='$otu_group'
+   #end if
+  #end if
+ </command>
+ <inputs>
+  <conditional name="input">
+   <param name="source" type="select" label="Generate principle components for">
+    <option value="similarity">OTU list</option>
+    <option value="shared">OTU Shared</option>
+   </param>
+   <when value="similarity">
+     <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
+     <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/>
+     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
+      <options from_dataset="otu_group">
+       <column name="name" index="1"/>
+       <column name="value" index="1"/>
+       <filter type="unique_value" name="unq_grp" column="1" />
+      </options>
+     </param>
+   </when>
+   <when value="shared">
+     <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
+     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
+      <options from_dataset="otu">
+       <column name="name" index="1"/>
+       <column name="value" index="1"/>
+       <filter type="unique_value" name="unq_grp" column="1" />
+      </options>
+     </param>
+   </when>
+  </conditional>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="groups" name="bootgroups" label="${tool.name} on ${on_string}: bootGroups" />
+ </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 get.group_ command generate principle components plot data.
+
+.. _get.group: http://www.mothur.org/wiki/Get.group
+
+ </help>
+</tool>