# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1326990844 21600
# Node ID ed906f8149bb3f3fc5f53dd293ff57ac17248605
# Parent  97e35ab2887cc63cd96c10970ee1c0d43e04a625
Mothur - html escape amperand in calculator option label

diff -r 97e35ab2887c -r ed906f8149bb mothur/tools/mothur/collect.shared.xml
--- a/mothur/tools/mothur/collect.shared.xml	Tue Jan 17 14:42:27 2012 -0600
+++ b/mothur/tools/mothur/collect.shared.xml	Thu Jan 19 10:34:04 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_collect_shared" name="Collect.shared" version="1.20.0" force_history_refresh="True">
+<tool id="mothur_collect_shared" name="Collect.shared" version="1.23.0" force_history_refresh="True">
  <description>Generate collector's curves for calculators on OTUs</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -67,7 +67,7 @@
    <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
    <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
    <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
-   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
+   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
    <option value="canberra">canberra - Community Structure Similarity -</option>
    <option value="gower">gower - Community Structure Similarity -</option>
    <option value="hellinger">hellinger - Community Structure Similarity -</option>
diff -r 97e35ab2887c -r ed906f8149bb mothur/tools/mothur/dist.shared.xml
--- a/mothur/tools/mothur/dist.shared.xml	Tue Jan 17 14:42:27 2012 -0600
+++ b/mothur/tools/mothur/dist.shared.xml	Thu Jan 19 10:34:04 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_dist_shared" name="Dist.shared" version="1.20.0" force_history_refresh="True">
+<tool id="mothur_dist_shared" name="Dist.shared" version="1.23.0" force_history_refresh="True">
  <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -76,7 +76,7 @@
    <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
    <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
    <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
-   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
+   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
    <option value="canberra">canberra - Community Structure Similarity -</option>
    <option value="gower">gower - Community Structure Similarity -</option>
    <option value="hellinger">hellinger - Community Structure Similarity -</option>
diff -r 97e35ab2887c -r ed906f8149bb mothur/tools/mothur/heatmap.sim.xml
--- a/mothur/tools/mothur/heatmap.sim.xml	Tue Jan 17 14:42:27 2012 -0600
+++ b/mothur/tools/mothur/heatmap.sim.xml	Thu Jan 19 10:34:04 2012 -0600
@@ -71,7 +71,7 @@
       <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
       <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
       <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
-      <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
+      <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
      </param>
    </when>
    <when value="column">
diff -r 97e35ab2887c -r ed906f8149bb mothur/tools/mothur/summary.qual.xml
--- a/mothur/tools/mothur/summary.qual.xml	Tue Jan 17 14:42:27 2012 -0600
+++ b/mothur/tools/mothur/summary.qual.xml	Thu Jan 19 10:34:04 2012 -0600
@@ -13,7 +13,7 @@
  </command>
  <inputs>
   <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
-  <param name="name" type="data" format="names" optional="true" label="name - Names" optional="true"/>
+  <param name="name" type="data" format="names" optional="true" label="name - Names"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
diff -r 97e35ab2887c -r ed906f8149bb mothur/tools/mothur/summary.shared.xml
--- a/mothur/tools/mothur/summary.shared.xml	Tue Jan 17 14:42:27 2012 -0600
+++ b/mothur/tools/mothur/summary.shared.xml	Thu Jan 19 10:34:04 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_summary_shared" name="Summary.shared" version="1.20.0"  force_history_refresh="True">
+<tool id="mothur_summary_shared" name="Summary.shared" version="1.23.0"  force_history_refresh="True">
  <description>Summary of calculator values for OTUs</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -64,7 +64,7 @@
    <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
    <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
    <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
-   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
+   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
    <option value="canberra">canberra - Community Structure Similarity -</option>
    <option value="gower">gower - Community Structure Similarity -</option>
    <option value="hellinger">hellinger - Community Structure Similarity -</option>
diff -r 97e35ab2887c -r ed906f8149bb mothur/tools/mothur/tree.shared.xml
--- a/mothur/tools/mothur/tree.shared.xml	Tue Jan 17 14:42:27 2012 -0600
+++ b/mothur/tools/mothur/tree.shared.xml	Thu Jan 19 10:34:04 2012 -0600
@@ -1,4 +1,4 @@
-<tool id="mothur_tree_shared" name="Tree.shared" version="1.20.0" force_history_refresh="True">
+<tool id="mothur_tree_shared" name="Tree.shared" version="1.23.0" force_history_refresh="True">
  <description>Generate a newick tree for dissimilarity among groups</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -95,7 +95,7 @@
    <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
    <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
    <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
-   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue & Clayton theta similarity coefficient</option>
+   <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
    <option value="canberra">canberra - Community Structure Similarity -</option>
    <option value="gower">gower - Community Structure Similarity -</option>
    <option value="hellinger">hellinger - Community Structure Similarity -</option>