diff mothur/tools/mothur/split.groups.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/split.groups.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/split.groups.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_split_groups" name="Split.groups" version="1.16.0" force_history_refresh="True">
+<tool id="mothur_split_groups" name="Split.groups" version="1.19.0" force_history_refresh="True">
  <description>Generates a fasta file for each group</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -6,13 +6,27 @@
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+?\.(\S+\.fasta)$:fasta'
+  --new_datasets='^\S+?\.(\S+\.fasta)$:fasta','^\S+?\.(\S+\.names)$:names'
   --fasta=$fasta
   --group=$group
+  #if $name.__str__ != "None" and len($name.__str__) > 0:
+   --name=$name
+  #end if
+  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
+   --groups=$groups
+  #end if
  </command>
  <inputs>
-  <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
+  <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
+  <param name="name" type="data" format="names" label="name - Names to split by group" optional="true"/>
   <param name="group" type="data" format="groups" label="group - Groups"/>
+  <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
+   <options from_dataset="group">
+    <column name="name" index="1"/>
+    <column name="value" index="1"/>
+    <filter type="unique_value" name="unq_grp" column="1" />
+   </options>
+  </param>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -33,8 +47,10 @@
 
 **Command Documenation**
 
-The split.groups_ command reads a fasta file group file and generates a fasta file for each group in the groupfile. 
+The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile.  A name_ file can also be split into groups.
 
+.. _group: http://www.mothur.org/wiki/Group_file
+.. _name: http://www.mothur.org/wiki/Name_file
 .. _split.groups: http://www.mothur.org/wiki/Split.groups
 
  </help>