diff mothur/tools/mothur/classify.otu.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/classify.otu.xml	Tue Jun 07 17:32:23 2011 -0400
+++ b/mothur/tools/mothur/classify.otu.xml	Tue Jun 07 17:35:35 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_classify_otu" name="Classify.otu" version="1.15.0" force_history_refresh="True">
+<tool id="mothur_classify_otu" name="Classify.otu" version="1.16.0" force_history_refresh="True">
  <description>Assign sequences to taxonomy</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -9,6 +9,9 @@
   --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy'
   --list=$otu
   --taxonomy=$tax.taxonomy
+  #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0:
+   --reftaxonomy=$reftax.taxonomy
+  #end if
   #if 100 >= int($cutoff.__str__) > 0:
    --cutoff=$cutoff
   #end if
@@ -36,13 +39,34 @@
     <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy Reference"/>
    </when>
   </conditional>
+  <conditional name="reftax">
+   <param name="source" type="select" label="Select Taxonomy from" help="">
+    <option value="none">None</option>
+    <option value="hist">History</option>
+    <option value="ref">Cached Reference</option>
+   </param>
+   <when value="none"/>
+   <when value="ref">
+    <param name="taxonomy" type="select" format="taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
+     <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="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
+   </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="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100">
+   <validator type="in_range" message="Confindence percentage cutoff must be between 0 and 100" min="0" max="100"/>
+  </param>
   <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/>
  </inputs>
  <outputs>