diff mothur/tools/mothur/get.sabund.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/get.sabund.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -0,0 +1,55 @@
+<tool id="mothur_get_sabund" name="Get.sabund" version="1.19.0">
+ <description>Get sabund from a otu list or rabund</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='get.sabund'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund
+  --outputdir='$logfile.extra_files_path'
+  #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
+   --list=$otu
+  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
+   --rabund=$otu
+  #end if
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label=$label
+  #end if
+ </command>
+ <inputs>
+  <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/>
+  <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
+   <options from_dataset="otu">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+   </options>
+  </param>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
+ </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.sabund_ command generates an sabund_ file from a list_ or rabund_ file.
+
+.. _sabund: http://www.mothur.org/wiki/Sabund_file
+.. _list: http://www.mothur.org/wiki/List_file
+.. _rabund: http://www.mothur.org/wiki/Rabund_file
+.. _get.sabund: http://www.mothur.org/wiki/Get.sabund
+
+
+ </help>
+</tool>