diff mothur/tools/mothur/merge.groups.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/merge.groups.xml	Tue Jun 07 17:35:35 2011 -0400
@@ -0,0 +1,100 @@
+<tool id="mothur_merge_groups" name="Merge.groups" version="1.16.0" >
+ <description>Merge groups in a shared file</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='merge.groups'
+  ## 98_sq_phylip_amazon.fn.merge.shared
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.merge\.\S+$:'$shared
+  --outputdir='$logfile.extra_files_path'
+  --shared=$otu
+  #if $design.source == 'hist':
+   --design=$design_dataset
+  #else:
+   --design=$generated_design
+  #end if
+  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
+   --groups=$groups
+  #end if
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label='$label'
+  #end if
+ </command>
+ <inputs>
+  <param name="otu" type="data" format="shared" label="shared - OTU Shared Dataset"/>
+  <param name="groups" type="select" optional="true" label="groups - Pick groups to include" 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>
+  <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true">
+   <options from_dataset="otu">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+    <filter type="unique_value" name="unq_lbl" column="0" />
+   </options>
+  </param>
+  <conditional name="design">
+   <param name="source" type="select" label="Grouping Design from" help="">
+    <option value="hist">Your History</option>
+    <option value="build">Build a grouping design</option>
+   </param>
+   <when value="hist">
+    <param name="design_dataset" type="data" format="tabular" label="design - assign groups to new grouping"
+           help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
+   </when>
+   <when value="build">
+    <repeat name="groupings" title="Grouping">
+     <param name="name" type="text" label="Name for a new combined grouping"/>
+     <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
+      <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>
+    </repeat>
+   </when>
+  </conditional> <!-- design -->
+ </inputs>
+ <configfiles>
+  <configfile name="generated_design">
+#if $design.source == 'build':
+#for $grouping in $design.groupings:
+#set grp_str = $grouping.groups.__str__
+#if grp_str != None and len(grp_str) > 0:
+#for $grp in grp_str.split(','):
+$grp	$grouping.name
+#end for
+#end if
+#end for
+#end if
+  </configfile>
+ </configfiles>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="shared" name="shared" label="${tool.name} on ${on_string}: merge.shared" />
+ </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 merge.groups_ command reads a shared file and a design file and merges the groups in the shared file that are in the same grouping in the design file.
+
+.. _merge.groups: http://www.mothur.org/wiki/Merge.groups
+
+ </help>
+</tool>