diff mothur/tools/mothur/get.sabund.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

--- a/mothur/tools/mothur/get.sabund.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tools/mothur/get.sabund.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,54 +1,59 @@
-<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=$label
-  #end if
- </command>
- <inputs>
-  <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/>
-  <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
-   <options>
-    <filter type="data_meta" ref="otu" key="labels" />
-   </options>
-  </param>
- </inputs>
- <outputs>
-  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
- </outputs>
- <requirements>
-  <requirement type="package" version="1.27">mothur</requirement>
- </requirements>
- <tests>
- </tests>
- <help>
-**Mothur Overview**
+<tool id="mothur_get_sabund" name="Get.sabund" version="1.20.0">
+	<description>Get sabund from a otu list or rabund</description>
+	<command interpreter="python">
+		mothur_wrapper.py 
+		--cmd='get.sabund'
+		--result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund
+		--outputdir='$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
+		#if $count.__str__ != "None" and len($count.__str__) > 0:
+		--count=$count
+		#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>
+				<filter type="data_meta" ref="otu" key="labels" />
+			</options>
+		</param>
+		<param name = "count" type="data" format="count_table" optional="true" help ="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/>
 
-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
+	</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="package" version="1.33">mothur</requirement>
+	</requirements>
+	<tests>
+	</tests>
+	<help>
+		**Mothur Overview**
 
-**Command Documenation**
+		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.
 
-The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file.
+		.. _Mothur: http://www.mothur.org/wiki/Main_Page
 
-.. _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
+		**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>
+	</help>
 </tool>