diff mothur/tools/mothur/sens.spec.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/sens.spec.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -0,0 +1,70 @@
+<tool id="mothur_sens_spec" name="Sens.spec" version="1.19.0" >
+ <description>Determine the quality of OTU assignment</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  #import re, os.path
+  --cmd='sens.spec'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sensspec$:'$sensspec
+  --outputdir='$logfile.extra_files_path'
+  --list=$list
+  #if isinstance($dist.datatype, $__app__.datatypes_registry.get_datatype_by_extension('pair.dist').__class__):
+   --column=$dist
+  #else
+   --phylip=$dist
+  #end if
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label='$label'
+  #end if
+  #if len($precision.__str__) > 0:
+   --precision=$precision
+  #end if
+  #if float($cutoff.__str__) > 0.0:
+   --cutoff=$cutoff
+  #end if
+  $hard
+ </command>
+ <inputs>
+  <param name="list" type="data" format="list" label="list - OTU List"/>
+  <param name="dist" type="data" format="dist" label="phylip,column - Distance Matrix"/>
+  <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" 
+     help="By default all are included if no selection is made.">
+   <options from_dataset="list">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+   </options>
+  </param>
+  <param name="precision" type="integer" value="100" optional="true" label="precision - Precision for rounding distance values"/>
+  <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" 
+                 help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
+  <param name="hard" type="boolean" checked="false" truevalue="--hard=true" falsevalue="" label="hard - Use hard cutoff instead of rounding"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="tabular" name="sensspec" label="${tool.name} on ${on_string}: sensspec" />
+ </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 sens.spec_ command takes a list_ and either a column_  or phylip_ distance matrix to determine the quality of OTU assignment.
+
+
+.. _list: http://www.mothur.org/wiki/List_file
+.. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix
+.. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _sens.spec: http://www.mothur.org/wiki/Sens.spec
+
+ </help>
+</tool>