# HG changeset patch
# User clustalomega
# Date 1311340142 14400
# Node ID bb1847435ec1e5f8dfead6d70ff540443d91cc05
# Parent  bc707542e5de006ee09ab2af3a2ef34dc51cd7ed
Uploaded

diff -r bc707542e5de -r bb1847435ec1 clustalomega/rgClustalOmega.xml
--- a/clustalomega/rgClustalOmega.xml	Thu Jul 21 13:35:08 2011 -0400
+++ b/clustalomega/rgClustalOmega.xml	Fri Jul 22 09:09:02 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="clustalomega" name="Clustal Omega" version="0.2">
+<tool id="clustalomega" name="Clustal Omega" version="1.0.2">
 <description>
 multiple sequence alignment program for proteins
 </description>
@@ -18,24 +18,21 @@
      --dealign
     #end if
     #if ($advanced.mbed.value=="Yes")
-     --mbed
+     --full
     #end if
     #if ($advanced.iteration.iteroptions =="true")
         --iter $advanced.iteration.iters
         #if ($advanced.iteration.mbediter.value=="Yes")
-         --mbed-iter
+         --full-iter
         #end if
         #if ($advanced.iteration.separateiters.separateiteroptions =="true")
          --max-guidetree-iterations=$advanced.iteration.separateiters.gtiters
          --max-hmm-iterations=$advanced.iteration.separateiters.hmmiters
         #end if
     #end if
-    #if ($advanced.dotree.value=="Yes")
-     --guidetree-out=$outtree
-    #end if
-    #if ($advanced.domatrix.value=="Yes")
-     --distmat-out=$outmatrix
-    #end if
+#end if
+#if ($dotree.value=="Yes")
+ --guidetree-out=$outtree
 #end if
 
 </command>
@@ -112,10 +109,9 @@
         <help>If given already aligned sequences, by default Clustal Omega use the existing alignment to guide creation of the new alignment, by constructing a HMM from the existing alignment. Check this box to realign aligned sequences from scratch.</help>
         </param>
 
-        <param name="mbed" type="select" display="checkboxes" multiple="True" label="Use mBed">
+        <param name="mbed" type="select" display="checkboxes" multiple="True" label="Calculate full distance matrix">
         <option value="Yes">Yes</option>
-            <help>Use embedding to calculate the guide tree more quickly and using less memory. Should be turned on 
-            when more than a thousand sequences are used.</help>
+            <help>By default, only a fraction of the distance matrix is calculated, for speed. Check this box to calculate a full distance matrix (slower and needs more memory, may be more accurate under some circumstances).</help>
         </param>
         
         <conditional name="iteration">
@@ -131,7 +127,7 @@
           <when value="true">
             <param name="iters" type="integer" value="1" label="Number of iterations"></param>
 
-            <param name="mbediter" type="select" display="checkboxes" multiple="True" label="Use MBED for iteration">
+            <param name="mbediter" type="select" display="checkboxes" multiple="True" label="Calculate full distance matrix during iteration">
                 <option value="Yes">Yes</option>
             </param>
                 <conditional name="separateiters">
@@ -155,9 +151,7 @@
       </when>
       </conditional>
         <param name="dotree" type="select" display="checkboxes" multiple="True" label="Output guide tree">
-            <option value="Yes">Yes</option>
-        </param>
-        <param name="domatrix" type="select" display="checkboxes" multiple="True" label="Output distance matrix">
+        <help>Outputs a guide tree in Newick format</help>
             <option value="Yes">Yes</option>
         </param>
 </inputs>
@@ -168,9 +162,6 @@
     <data format="txt" name="outtree" label="${outname}_guidetree.txt">
         <filter>dotree=="Yes"</filter>
     </data>
-    <data format="txt" name="outmatrix" label="${outname}_distances.txt">
-        <filter>domatrix=="Yes"</filter>
-    </data>
 </outputs>
 
 <tests>
@@ -208,7 +199,7 @@
 "external profile alignment" or EPA.
 
 Clustal-Omega uses HMMs for the alignment engine, based on the HHalign
-package from Johannes Soeding [1].  Guide trees are optionally made
+package from Johannes Soeding [1].  Guide trees are made by default
 using mBed [2] which can cluster very large numbers of sequences in
 O(N*log(N)) time.  Multiple alignment then proceeds by aligning larger
 and larger alignments using HHalign, following the clustering given by
@@ -224,12 +215,9 @@
 
 A standalone version of Clustal Omega for Linux/Windows/Mac is available from http://www.clustal.org/
 
-[1] Johannes Soding (2005) Protein homology detection by HMM-HMM
-    comparison. Bioinformatics 21 (7): 951–960.
+[1] Johannes Soding (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.
 
-[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG.  Sequence
-    embedding for fast construction of guide trees for multiple
-    sequence alignment.  Algorithms Mol Biol. 2010 May 14;5:21.
+[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG.  Sequence embedding for fast construction of guide trees for multiple sequence alignment.  Algorithms Mol Biol. 2010 May 14;5:21.
 
 </help>
 </tool>