diff mothur/tools/mothur/read.otu.xml @ 0:3202a38e44d9

Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/read.otu.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,55 @@
+<tool id="mothur_read_otu" name="Read.otu" version="1.15.0" force_history_refresh="True">
+ <description>Read OTU list and group to create a shared file</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='read.otu'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared:'$shared
+  --outputdir='$logfile.extra_files_path'
+  #if $show_rabund.value == True:
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 
+   --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund'
+  #end if
+  --cmd='read.otu'
+  --list=$otu
+  --group=$otu_group
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label='$label'
+  #end if
+ </command>
+ <inputs>
+  <param name="otu" type="data" format="list" label="list - OTU List"/>
+  <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/>
+  <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
+   <options from_dataset="otu">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+   </options>
+  </param>
+  <param name="show_rabund" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Put Group rabund files in your history"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${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 read.otu_ command is called before most of the OTU based mothur commands.  It is included here explicitly to allow the creatation of a shared file from OTU list and group files.  
+
+.. _read.otu: http://www.mothur.org/wiki/Read.otu
+
+ </help>
+</tool>