diff mothur/tools/mothur/make.shared.xml @ 2:e990ac8a0f58

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/make.shared.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -0,0 +1,75 @@
+<tool id="mothur_make_shared" name="Make.shared" version="1.19.0" force_history_refresh="True">
+ <description>Make a shared file from a list and a group</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  #import re, os.path
+  --cmd='make.shared'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared$:'$shared
+  --outputdir='$logfile.extra_files_path'
+  #if $as_datasets.__str__ == "yes":
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund'
+  #end if
+  --list=$list
+  --group=$group
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label='$label'
+  #end if
+  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
+    --unique=$groups
+  #end if
+  #if $ordergroup.__str__ != "None" and len($ordergroup.__str__) > 0:
+   --ordergroup=$ordergroup
+  #end if
+ </command>
+ <inputs>
+  <param name="list" type="data" format="list" label="list - OTU List"/>
+  <param name="group" type="data" format="groups" label="group - "/>
+  <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" 
+     help="By default all are included if no selection is made.">
+   <options from_dataset="list">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+   </options>
+  </param>
+  <param name="groups" type="select" label="groups - Groups to include" multiple="true">
+   <options from_dataset="group">
+     <column name="name" index="1"/>
+     <column name="value" index="1"/>
+     <filter type="unique_value" name="unq_grp" column="1" />
+   </options>
+  </param>
+  <param name="ordergroup" type="data" format="groups" optional="true" label="ordergroup - one column list of group names in desired order"/>
+  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each group rabund"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="shared" name="shared" label="${tool.name} on ${on_string}: 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 make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group.
+
+
+.. _list: http://www.mothur.org/wiki/List_file
+.. _group: http://www.mothur.org/wiki/Group_file
+.. _shared: http://www.mothur.org/wiki/Shared_file
+.. _rabund: http://www.mothur.org/wiki/Rabund_file
+.. _make.shared: http://www.mothur.org/wiki/Make.shared
+
+ </help>
+</tool>