diff mothur/tools/mothur/classify.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/classify.otu.xml	Tue Jun 07 17:32:23 2011 -0400
@@ -0,0 +1,73 @@
+<tool id="mothur_classify_otu" name="Classify.otu" version="1.15.0" force_history_refresh="True">
+ <description>Assign sequences to taxonomy</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='classify.otu'
+  --result='^mothur.\S+\.logfile$:'$logfile
+  --outputdir='$logfile.extra_files_path'
+  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+  --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy'
+  --list=$otu
+  --taxonomy=$tax.taxonomy
+  #if 100 >= int($cutoff.__str__) > 0:
+   --cutoff=$cutoff
+  #end if
+  #if $label.__str__ != "None" and len($label.__str__) > 0:
+   --label='$label'
+  #end if
+  $probs
+ </command>
+ <inputs>
+  <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List "/>
+  <conditional name="tax">
+   <param name="source" type="select" label="Select Taxonomy from" help="">
+    <option value="hist">History</option>
+    <option value="ref">Cached Reference</option>
+   </param>
+   <when value="ref">
+    <param name="taxonomy" type="select" format="taxonomy" label="taxonomy - Taxonomy Reference">
+     <options from_file="mothur_taxonomy.loc">
+      <column name="name" index="0" />
+      <column name="value" index="1" />
+     </options>
+    </param>
+   </when>
+   <when value="hist">
+    <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy Reference"/>
+   </when>
+  </conditional>
+  <param name="label" type="select" label="label - OTU Labels" multiple="true">
+   <options from_dataset="otu">
+    <column name="name" index="0"/>
+    <column name="value" index="0"/>
+   </options>
+  </param>
+  <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100"/>
+  <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+ </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 classify.otu_ command assigns sequences to chosen taxonomy outline.
+
+.. _classify.otu: http://www.mothur.org/wiki/Classify.otu
+
+
+ </help>
+</tool>