diff mothur/tools/mothur/summary.tax.xml @ 15:a6189f58fedb

Mothur - updated for Mothur version 1.22.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tools/mothur/summary.tax.xml	Tue Nov 08 11:45:32 2011 -0600
@@ -0,0 +1,84 @@
+<tool id="mothur_summary_tax" name="Summary.tax" version="1.22.0">
+ <description>Assign sequences to taxonomy</description>
+ <command interpreter="python">
+  mothur_wrapper.py 
+  --cmd='summary.tax'
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tax\.summary$:'$tax_summary
+  --outputdir='$logfile.extra_files_path'
+  --taxonomy=$tax.taxonomy
+  #if $name.__str__ != "None" and len($name.__str__) > 0:
+   --name='$name'
+  #end if
+  #if $group.__str__ != "None" and len($group.__str__) > 0:
+   --group='$group'
+  #end if
+  #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0:
+   --reftaxonomy=$reftax.taxonomy
+  #end if
+ </command>
+ <inputs>
+  <conditional name="tax">
+   <param name="source" type="select" label="Select Taxonomy from" help="">
+    <option value="hist">History</option>
+    <option value="ref">Cached Reference</option>
+   </param>
+   <when value="ref">
+    <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy Reference">
+     <options from_file="mothur_taxonomy.loc">
+      <column name="name" index="0" />
+      <column name="value" index="1" />
+     </options>
+    </param>
+   </when>
+   <when value="hist">
+    <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"/>
+   </when>
+  </conditional>
+  <param name="name" type="data" format="names" optional="true" label="name - taxonomy sequence names"/>
+  <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/>
+  <conditional name="reftax">
+   <param name="source" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
+    <option value="none">Selection is Optional</option>
+    <option value="hist">History</option>
+    <option value="ref">Cached Reference</option>
+   </param>
+   <when value="none"/>
+   <when value="ref">
+    <param name="taxonomy" type="select" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
+     <options from_file="mothur_taxonomy.loc">
+      <column name="name" index="0" />
+      <column name="value" index="1" />
+     </options>
+    </param>
+   </when>
+   <when value="hist">
+    <param name="taxonomy" type="data" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
+   </when>
+  </conditional>
+ </inputs>
+ <outputs>
+  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
+  <data format="summary" name="tax_summary" label="${tool.name} on ${on_string}: summary" />
+ </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 summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information.
+
+.. _summary.tax: http://www.mothur.org/wiki/Summary.otu
+
+ </help>
+</tool>