diff mothur/tools/mothur/classify.otu.xml @ 2:e990ac8a0f58

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/classify.otu.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/classify.otu.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_classify_otu" name="Classify.otu" version="1.16.0" force_history_refresh="True">
+<tool id="mothur_classify_otu" name="Classify.otu" version="1.19.0" force_history_refresh="True">
  <description>Assign sequences to taxonomy</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -6,7 +6,7 @@
   --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'
+  --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary'
   --list=$otu
   --taxonomy=$tax.taxonomy
   #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0:
@@ -18,6 +18,10 @@
   #if $label.__str__ != "None" and len($label.__str__) > 0:
    --label='$label'
   #end if
+  #if $group.__str__ != "None" and len($group.__str__) > 0:
+   --group='$group'
+  #end if
+  --basis=$basis
   $probs
  </command>
  <inputs>
@@ -28,7 +32,7 @@
     <option value="ref">Cached Reference</option>
    </param>
    <when value="ref">
-    <param name="taxonomy" type="select" format="taxonomy" label="taxonomy - Taxonomy Reference">
+    <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy Reference">
      <options from_file="mothur_taxonomy.loc">
       <column name="name" index="0" />
       <column name="value" index="1" />
@@ -36,7 +40,7 @@
     </param>
    </when>
    <when value="hist">
-    <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy Reference"/>
+    <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
    </when>
   </conditional>
   <conditional name="reftax">
@@ -47,7 +51,7 @@
    </param>
    <when value="none"/>
    <when value="ref">
-    <param name="taxonomy" type="select" format="taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
+    <param name="taxonomy" type="select" format="seq.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" />
@@ -55,7 +59,7 @@
     </param>
    </when>
    <when value="hist">
-    <param name="taxonomy" type="data" format="taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
+    <param name="taxonomy" type="data" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
    </when>
   </conditional>
   <param name="label" type="select" label="label - OTU Labels" multiple="true">
@@ -68,6 +72,11 @@
    <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"/>
+  <param name="basis" type="select" label="basis - Summary file gives numbers of" help="">
+   <option value="otu">OTU</option>
+   <option value="sequence">sequence</option>
+  </param>
+  <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
@@ -90,6 +99,8 @@
 
 The classify.otu_ command assigns sequences to chosen taxonomy outline.
 
+The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu. For example consider the following basis=sequence could give Clostridiales 3 105 16 43 46, where 105 is the total number of sequences whose otu classified to Clostridiales. 16 is the number of sequences in the otus from groupA, 43 is the number of sequences in the otus from groupB, and 46 is the number of sequences in the otus from groupC. Now for basis=otu could give Clostridiales 3 7 6 1 2, where 7 is the number of otus that classified to Clostridiales. 6 is the number of otus containing sequences from groupA, 1 is the number of otus containing sequences from groupB, and 2 is the number of otus containing sequences from groupC.
+
 .. _classify.otu: http://www.mothur.org/wiki/Classify.otu