# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1346898523 18000
# Node ID a9d51d14f9e961d63b11fa30f93ac7470e353057
# Parent  6b358d0f17b40201ed59ac30e2a2d273ec71bc94
Add tool_dependencies

diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tool_dependencies.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -0,0 +1,35 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="mothur" version="1.24.0">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://www.mothur.org/w/images/0/09/Mothur.1.24.1.zip</action>
+                <action type="shell_command">cd Mothur.source</action>
+                <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>mothur</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>uchime</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+These links provide information for building the Mothur package in most environments .
+
+http://www.mothur.org/wiki/Download_mothur
+
+http://www.mothur.org/wiki/Installation
+
+http://www.mothur.org/wiki/Makefile_options
+
+        </readme>
+    </package>
+</tool_dependency>
+
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/align.check.xml
--- a/mothur/tools/mothur/align.check.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/align.check.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -33,7 +33,7 @@
   <data format="align.check" name="out_file" label="${tool.name} on ${on_string}: align.check"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/align.seqs.xml
--- a/mothur/tools/mothur/align.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/align.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -96,7 +96,7 @@
   <data format="align.report" name="report" label="${tool.name} on ${on_string}: align.report" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/amova.xml
--- a/mothur/tools/mothur/amova.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/amova.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -26,7 +26,7 @@
   <data format="tabular" name="amova" label="${tool.name} on ${on_string}: amova"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/anosim.xml
--- a/mothur/tools/mothur/anosim.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/anosim.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -26,7 +26,7 @@
   <data format="tabular" name="anosim" label="${tool.name} on ${on_string}: anosim"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/bin.seqs.xml
--- a/mothur/tools/mothur/bin.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/bin.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -34,7 +34,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/bootstrap.shared.xml
--- a/mothur/tools/mothur/bootstrap.shared.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/bootstrap.shared.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -1,126 +0,0 @@
-<tool id="mothur_bootstrap_shared" name="Bootstrap.shared" version="1.16.0" force_history_refresh="True">
- <description>Generate a newick trees for dissimilarity among groups</description>
- <command interpreter="python">
-  #*
-98_sq_phylip_amazon.fn.jclass.bootunique.tre
-98_sq_phylip_amazon.fn.thetayc.bootunique.tre
-98_sq_phylip_amazon.fn.jclass.bootunique.cons.pairs
-98_sq_phylip_amazon.fn.jclass.bootunique.cons.tre
-98_sq_phylip_amazon.fn.thetayc.bootunique.cons.pairs
-98_sq_phylip_amazon.fn.thetayc.bootunique.cons.tre
-98_sq_phylip_amazon.fn.jclass.boot0.00.tre
-98_sq_phylip_amazon.fn.thetayc.boot0.00.tre
-98_sq_phylip_amazon.fn.jclass.boot0.00.cons.pairs
-98_sq_phylip_amazon.fn.jclass.boot0.00.cons.tre
-98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.pairs
-98_sq_phylip_amazon.fn.thetayc.boot0.00.cons.tre
-  *#
-  mothur_wrapper.py 
-  --cmd='bootstrap.shared'
-  --result='^mothur.\S+\.logfile$:'$logfile
-  --outputdir='$logfile.extra_files_path'
-  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.tre)$:tre','^\S+\.([a-z]+\.boot(unique|[0-9.]*)\.cons\.pairs)$:txt'
-  --READ_cmd='read.otu'
-  #if $input.source == 'similarity':
-   --READ_list=$input.otu
-   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
-    --READ_group='$otu_group'
-   #end if
-   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
-    --READ_label='$input.label'
-   #end if
-  #elif $input.source == 'shared':
-   --READ_shared=$input.otu
-   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
-    --READ_label='$input.label'
-   #end if
-  #end if
-  #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
-   --groups=$input.groups
-  #end if
-  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
-   --calc=$calc
-  #end if
-  #if int($iters.__str__) > 0:
-   --iters=$iters
-  #end if
- </command>
- <inputs>
-  <!-- list,group  or shared -->
-  <conditional name="input">
-   <param name="source" type="select" label="Generate Heatmap for">
-    <option value="similarity">OTU list</option>
-    <option value="shared">OTU Shared</option>
-   </param>
-   <when value="similarity">
-     <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
-     <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/>
-     <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="groups" type="select" label="groups - Groups to consider" multiple="true">
-      <options from_dataset="otu_group">
-       <column name="name" index="1"/>
-       <column name="value" index="1"/>
-       <filter type="unique_value" name="unq_grp" column="1" />
-      </options>
-     </param>
-   </when>
-   <when value="shared">
-     <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
-     <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"/>
-       <filter type="unique_value" name="unq_lbl" column="0" />
-      </options>
-     </param>
-     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
-      <options from_dataset="otu">
-       <column name="name" index="1"/>
-       <column name="value" index="1"/>
-       <filter type="unique_value" name="unq_grp" column="1" />
-      </options>
-     </param>
-   </when>
-  </conditional>
-  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
-   <options from_file="mothur_calculators.loc">
-     <column name="mult2" index="2"/>
-     <column name="name" index="0"/>
-     <column name="value" index="0"/>
-     <filter type="static_value" name="mult2" column="2" value="shar" />
-   </options>
-  </param>
-  <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
- </inputs>
- <outputs>
-  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
- </outputs>
- <requirements>
-  <requirement type="binary">mothur</requirement>
- </requirements>
- <tests>
- </tests>
- <help>
-**Mothur Overview**
-
-Mothur_, initiated by Dr. Patrick Schloss and his software development team
-in the Department of Microbiology and Immunology at The University of Michigan,
-provides bioinformatics for the microbial ecology community.
-
-.. _Mothur: http://www.mothur.org/wiki/Main_Page
-
-**Command Documenation**
-
-The bootstrap.shared_ command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups.
-
-.. _bootstrap.shared: http://www.mothur.org/wiki/Bootstrap.shared
-
-
- </help>
-</tool>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/chimera.bellerophon.xml
--- a/mothur/tools/mothur/chimera.bellerophon.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/chimera.bellerophon.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -31,7 +31,7 @@
   <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: bellerophon.accnos" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/chimera.ccode.xml
--- a/mothur/tools/mothur/chimera.ccode.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/chimera.ccode.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -64,7 +64,7 @@
   <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: ccode.accnos" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/chimera.check.xml
--- a/mothur/tools/mothur/chimera.check.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/chimera.check.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -64,7 +64,7 @@
   <data format="txt" name="out_file" label="${tool.name} on ${on_string}: chimeracheck.chimeras" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/chimera.perseus.xml
--- a/mothur/tools/mothur/chimera.perseus.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/chimera.perseus.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -34,7 +34,7 @@
   <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/chimera.pintail.xml
--- a/mothur/tools/mothur/chimera.pintail.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/chimera.pintail.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -122,7 +122,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/chimera.slayer.xml
--- a/mothur/tools/mothur/chimera.slayer.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/chimera.slayer.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -98,7 +98,7 @@
   <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: slayer.accnos" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/chimera.uchime.xml
--- a/mothur/tools/mothur/chimera.uchime.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/chimera.uchime.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -149,7 +149,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/chop.seqs.xml
--- a/mothur/tools/mothur/chop.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/chop.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -26,7 +26,7 @@
   <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: chop.fasta" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/classify.otu.xml
--- a/mothur/tools/mothur/classify.otu.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/classify.otu.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -85,7 +85,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/classify.seqs.xml
--- a/mothur/tools/mothur/classify.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/classify.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -121,7 +121,7 @@
   <data format="tax.summary" name="tax_summary" label="${tool.name} on ${on_string}: tax.summary" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/classify.tree.xml
--- a/mothur/tools/mothur/classify.tree.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/classify.tree.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -33,7 +33,7 @@
   <data format_source="tabular" name="summary" label="${tool.name} on ${on_string}: taxonomy.summary" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/clearcut.xml
--- a/mothur/tools/mothur/clearcut.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/clearcut.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -64,7 +64,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/cluster.classic.xml
--- a/mothur/tools/mothur/cluster.classic.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/cluster.classic.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -54,7 +54,7 @@
   <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/cluster.fragments.xml
--- a/mothur/tools/mothur/cluster.fragments.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/cluster.fragments.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -29,7 +29,7 @@
   <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/cluster.split.xml
--- a/mothur/tools/mothur/cluster.split.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/cluster.split.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -115,7 +115,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/cluster.xml
--- a/mothur/tools/mothur/cluster.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/cluster.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -72,7 +72,7 @@
   <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/collect.shared.xml
--- a/mothur/tools/mothur/collect.shared.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/collect.shared.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -85,7 +85,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/collect.single.xml
--- a/mothur/tools/mothur/collect.single.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/collect.single.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -79,7 +79,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/consensus.seqs.xml
--- a/mothur/tools/mothur/consensus.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/consensus.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -56,7 +56,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/cooccurrence.xml
--- a/mothur/tools/mothur/cooccurrence.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/cooccurrence.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -61,7 +61,7 @@
   <data format="tabular" name="out_summary" label="${tool.name} on ${on_string}: cooccurence.summary" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/corr.axes.xml
--- a/mothur/tools/mothur/corr.axes.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/corr.axes.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -65,7 +65,7 @@
   <data format="axes" name="corr_axes" label="${tool.name} on ${on_string}: corr.axes"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/count.groups.xml
--- a/mothur/tools/mothur/count.groups.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/count.groups.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -47,7 +47,7 @@
   <data format="tabular" name="grp_count" label="${tool.name} on ${on_string}: group.count" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/count.seqs.xml
--- a/mothur/tools/mothur/count.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/count.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -36,7 +36,7 @@
   <data format="tabular" name="seq_count" label="${tool.name} on ${on_string}: seq.count" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/create.database.xml
--- a/mothur/tools/mothur/create.database.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/create.database.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -38,7 +38,7 @@
   <data format="tabular" name="database" label="${tool.name} on ${on_string}: database" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/degap.seqs.xml
--- a/mothur/tools/mothur/degap.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/degap.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -15,7 +15,7 @@
   <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/deunique.seqs.xml
--- a/mothur/tools/mothur/deunique.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/deunique.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -17,7 +17,7 @@
   <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/deunique.tree.xml
--- a/mothur/tools/mothur/deunique.tree.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/deunique.tree.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -17,7 +17,7 @@
   <data format_source="tree" name="out_tree" label="${tool.name} on ${on_string}: deunique.tre" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/dist.seqs.xml
--- a/mothur/tools/mothur/dist.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/dist.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -49,7 +49,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/dist.shared.xml
--- a/mothur/tools/mothur/dist.shared.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/dist.shared.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -118,7 +118,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/fastq.info.xml
--- a/mothur/tools/mothur/fastq.info.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/fastq.info.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -22,7 +22,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/filter.seqs.xml
--- a/mothur/tools/mothur/filter.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/filter.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -57,7 +57,7 @@
   <data format="align" name="out_fasta" label="${tool.name} on ${on_string}: filtered fasta" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.group.xml
--- a/mothur/tools/mothur/get.group.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.group.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -15,7 +15,7 @@
   <data format="groups" name="bootgroups" label="${tool.name} on ${on_string}: bootGroups" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.groups.xml
--- a/mothur/tools/mothur/get.groups.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.groups.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -94,7 +94,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.lineage.xml
--- a/mothur/tools/mothur/get.lineage.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.lineage.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -73,7 +73,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.otulist.xml
--- a/mothur/tools/mothur/get.otulist.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.otulist.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -38,7 +38,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.oturep.xml
--- a/mothur/tools/mothur/get.oturep.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.oturep.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -90,7 +90,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.otus.xml
--- a/mothur/tools/mothur/get.otus.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.otus.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -55,7 +55,7 @@
   <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.rabund.xml
--- a/mothur/tools/mothur/get.rabund.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.rabund.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -30,7 +30,7 @@
   <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.relabund.xml
--- a/mothur/tools/mothur/get.relabund.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.relabund.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -42,7 +42,7 @@
   <data format="relabund" name="relabund" label="${tool.name} on ${on_string}: relabund" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.sabund.xml
--- a/mothur/tools/mothur/get.sabund.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.sabund.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -27,7 +27,7 @@
   <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.seqs.xml
--- a/mothur/tools/mothur/get.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -77,7 +77,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/get.sharedseqs.xml
--- a/mothur/tools/mothur/get.sharedseqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/get.sharedseqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -78,7 +78,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/hcluster.xml
--- a/mothur/tools/mothur/hcluster.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/hcluster.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -76,7 +76,7 @@
   <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/heatmap.bin.xml
--- a/mothur/tools/mothur/heatmap.bin.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/heatmap.bin.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -102,7 +102,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/heatmap.sim.xml
--- a/mothur/tools/mothur/heatmap.sim.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/heatmap.sim.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -86,7 +86,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/homova.xml
--- a/mothur/tools/mothur/homova.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/homova.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -26,7 +26,7 @@
   <data format="tabular" name="homova" label="${tool.name} on ${on_string}: homova"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/indicator.xml
--- a/mothur/tools/mothur/indicator.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/indicator.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -51,7 +51,7 @@
   <data format="tabular" name="summary" label="${tool.name} on ${on_string}: indicator.summary"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/libshuff.xml
--- a/mothur/tools/mothur/libshuff.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/libshuff.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -52,7 +52,7 @@
   <data format="tabular" name="coverage" label="${tool.name} on ${on_string}: coverage"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/list.seqs.xml
--- a/mothur/tools/mothur/list.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/list.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -55,7 +55,7 @@
   <data format="accnos" name="out_file" label="${tool.name} on ${on_string}: accnos" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/make.biom.xml
--- a/mothur/tools/mothur/make.biom.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/make.biom.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -45,7 +45,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/make.design.xml
--- a/mothur/tools/mothur/make.design.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/make.design.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -29,7 +29,7 @@
   <data format="design" name="design" label="${tool.name} on ${on_string}: design" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/make.fastq.xml
--- a/mothur/tools/mothur/make.fastq.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/make.fastq.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -24,7 +24,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/make.group.xml
--- a/mothur/tools/mothur/make.group.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/make.group.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -21,7 +21,7 @@
   <data format="groups" name="output" label="${tool.name} on ${on_string}: group" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/make.shared.xml
--- a/mothur/tools/mothur/make.shared.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/make.shared.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -48,7 +48,7 @@
   <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/make.shared_from_biom.xml
--- a/mothur/tools/mothur/make.shared_from_biom.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/make.shared_from_biom.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -31,7 +31,7 @@
   <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/mantel.xml
--- a/mothur/tools/mothur/mantel.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/mantel.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -27,7 +27,7 @@
   <data format="tabular" name="mantel" label="${tool.name} on ${on_string}: mantel"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/merge.files.xml
--- a/mothur/tools/mothur/merge.files.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/merge.files.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -54,7 +54,7 @@
   <data format="input" name="output" label="${tool.name} on ${on_string}: ${merge.type}"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/merge.groups.xml
--- a/mothur/tools/mothur/merge.groups.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/merge.groups.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -85,7 +85,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/metastats.xml
--- a/mothur/tools/mothur/metastats.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/metastats.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -55,7 +55,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/nmds.xml
--- a/mothur/tools/mothur/nmds.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/nmds.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -41,7 +41,7 @@
   <data format="tabular" name="stress_nmds" label="${tool.name} on ${on_string}: nmds.stress"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/normalize.shared.xml
--- a/mothur/tools/mothur/normalize.shared.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/normalize.shared.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -50,7 +50,7 @@
   <data format="shared" name="shared" label="${tool.name} on ${on_string}: norm.shared" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/otu.association.xml
--- a/mothur/tools/mothur/otu.association.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/otu.association.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -44,7 +44,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/otu.hierarchy.xml
--- a/mothur/tools/mothur/otu.hierarchy.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/otu.hierarchy.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -33,7 +33,7 @@
   <data format="tabular" name="hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/pairwise.seqs.xml
--- a/mothur/tools/mothur/pairwise.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/pairwise.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -74,7 +74,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/parse.list.xml
--- a/mothur/tools/mothur/parse.list.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/parse.list.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -27,7 +27,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/parsimony.xml
--- a/mothur/tools/mothur/parsimony.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/parsimony.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -47,7 +47,7 @@
   -->
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/pca.xml
--- a/mothur/tools/mothur/pca.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/pca.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -40,7 +40,7 @@
   <data format="txt" name="pca_loadings" label="${tool.name} on ${on_string}: pca.loadings" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/pcoa.xml
--- a/mothur/tools/mothur/pcoa.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/pcoa.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -18,7 +18,7 @@
   <data format="tabular" name="loadings" label="${tool.name} on ${on_string}: loadings" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/pcr.seqs.xml
--- a/mothur/tools/mothur/pcr.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/pcr.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -99,7 +99,7 @@
 
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/phylo.diversity.xml
--- a/mothur/tools/mothur/phylo.diversity.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/phylo.diversity.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -74,7 +74,7 @@
   -->
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/phylotype.xml
--- a/mothur/tools/mothur/phylotype.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/phylotype.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -41,7 +41,7 @@
   <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/pre.cluster.xml
--- a/mothur/tools/mothur/pre.cluster.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/pre.cluster.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -36,7 +36,7 @@
   <data format="tabular" name="map_out" label="${tool.name} on ${on_string}: precluster.map" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/rarefaction.shared.xml
--- a/mothur/tools/mothur/rarefaction.shared.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/rarefaction.shared.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -46,7 +46,7 @@
   <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/rarefaction.single.xml
--- a/mothur/tools/mothur/rarefaction.single.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/rarefaction.single.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -69,7 +69,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/read.otu.xml
--- a/mothur/tools/mothur/read.otu.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/read.otu.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -1,54 +0,0 @@
-<tool id="mothur_read_otu" name="Read.otu" version="1.16.0" force_history_refresh="True">
- <description>Read OTU list and group to create a shared file</description>
- <command interpreter="python">
-  mothur_wrapper.py 
-  --cmd='read.otu'
-  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared:'$shared
-  --outputdir='$logfile.extra_files_path'
-  #if $show_rabund.value == True:
-   --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 
-   --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund'
-  #end if
-  --list=$otu
-  --group=$otu_group
-  #if $label.__str__ != "None" and len($label.__str__) > 0:
-   --label='$label'
-  #end if
- </command>
- <inputs>
-  <param name="otu" type="data" format="list" label="list - OTU List"/>
-  <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/>
-  <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true">
-   <options from_dataset="otu">
-    <column name="name" index="0"/>
-    <column name="value" index="0"/>
-   </options>
-  </param>
-  <param name="show_rabund" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Put Group rabund files in your history"/>
- </inputs>
- <outputs>
-  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
-  <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" />
- </outputs>
- <requirements>
-  <requirement type="binary">mothur</requirement>
- </requirements>
- <tests>
- </tests>
- <help>
-**Mothur Overview**
-
-Mothur_, initiated by Dr. Patrick Schloss and his software development team
-in the Department of Microbiology and Immunology at The University of Michigan,
-provides bioinformatics for the microbial ecology community.
-
-.. _Mothur: http://www.mothur.org/wiki/Main_Page
-
-**Command Documenation**
-
-The read.otu_ command is called before most of the OTU based mothur commands.  It is included here explicitly to allow the creatation of a shared file from OTU list and group files.  
-
-.. _read.otu: http://www.mothur.org/wiki/Read.otu
-
- </help>
-</tool>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/remove.groups.xml
--- a/mothur/tools/mothur/remove.groups.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/remove.groups.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -94,7 +94,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/remove.lineage.xml
--- a/mothur/tools/mothur/remove.lineage.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/remove.lineage.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -73,7 +73,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/remove.otus.xml
--- a/mothur/tools/mothur/remove.otus.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/remove.otus.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -55,7 +55,7 @@
   <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/remove.rare.xml
--- a/mothur/tools/mothur/remove.rare.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/remove.rare.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -91,7 +91,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/remove.seqs.xml
--- a/mothur/tools/mothur/remove.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/remove.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -77,7 +77,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/reverse.seqs.xml
--- a/mothur/tools/mothur/reverse.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/reverse.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -15,7 +15,7 @@
   <data format_source="fasta" name="out_fasta" label="${tool.name} on ${on_string}: rc.fasta" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/screen.seqs.xml
--- a/mothur/tools/mothur/screen.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/screen.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -101,7 +101,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/sens.spec.xml
--- a/mothur/tools/mothur/sens.spec.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/sens.spec.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -42,7 +42,7 @@
   <data format="tabular" name="sensspec" label="${tool.name} on ${on_string}: sensspec" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/seq.error.xml
--- a/mothur/tools/mothur/seq.error.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/seq.error.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -146,7 +146,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/sffinfo.xml
--- a/mothur/tools/mothur/sffinfo.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/sffinfo.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -53,7 +53,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/shhh.flows.xml
--- a/mothur/tools/mothur/shhh.flows.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/shhh.flows.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -79,7 +79,7 @@
   <data format_source="tabular" name="shhh_counts" label="${tool.name} on ${on_string}: shhh.counts"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/shhh.seqs.xml
--- a/mothur/tools/mothur/shhh.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/shhh.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -32,7 +32,7 @@
   <data format_source="txt" name="shhh_map" label="${tool.name} on ${on_string}: shhh.map"/>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/sort.seqs.xml
--- a/mothur/tools/mothur/sort.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/sort.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -69,7 +69,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/split.abund.xml
--- a/mothur/tools/mothur/split.abund.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/split.abund.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -98,7 +98,7 @@
   -->
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/split.groups.xml
--- a/mothur/tools/mothur/split.groups.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/split.groups.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -30,7 +30,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/sub.sample.xml
--- a/mothur/tools/mothur/sub.sample.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/sub.sample.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -179,7 +179,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/summary.qual.xml
--- a/mothur/tools/mothur/summary.qual.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/summary.qual.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -20,7 +20,7 @@
   <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/summary.seqs.xml
--- a/mothur/tools/mothur/summary.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/summary.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -20,7 +20,7 @@
   <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/summary.shared.xml
--- a/mothur/tools/mothur/summary.shared.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/summary.shared.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -83,7 +83,7 @@
   <data format="tabular" name="summary" label="${tool.name} on ${on_string}: shared.summary" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/summary.single.xml
--- a/mothur/tools/mothur/summary.single.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/summary.single.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -81,7 +81,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/summary.tax.xml
--- a/mothur/tools/mothur/summary.tax.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/summary.tax.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -61,7 +61,7 @@
   <data format="summary" name="tax_summary" label="${tool.name} on ${on_string}: summary" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/tree.shared.xml
--- a/mothur/tools/mothur/tree.shared.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/tree.shared.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -136,7 +136,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/trim.flows.xml
--- a/mothur/tools/mothur/trim.flows.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/trim.flows.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -115,7 +115,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/trim.seqs.xml
--- a/mothur/tools/mothur/trim.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/trim.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -151,7 +151,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/unifrac.unweighted.xml
--- a/mothur/tools/mothur/unifrac.unweighted.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/unifrac.unweighted.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -110,7 +110,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/unifrac.weighted.xml
--- a/mothur/tools/mothur/unifrac.weighted.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/unifrac.weighted.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -117,7 +117,7 @@
   </data>
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/unique.seqs.xml
--- a/mothur/tools/mothur/unique.seqs.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/unique.seqs.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -20,7 +20,7 @@
   <data format="names" name="out_names" label="${tool.name} on ${on_string}: names" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>
diff -r 6b358d0f17b4 -r a9d51d14f9e9 mothur/tools/mothur/venn.xml
--- a/mothur/tools/mothur/venn.xml	Wed Sep 05 19:49:43 2012 -0500
+++ b/mothur/tools/mothur/venn.xml	Wed Sep 05 21:28:43 2012 -0500
@@ -88,7 +88,7 @@
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  </outputs>
  <requirements>
-  <requirement type="binary">mothur</requirement>
+  <requirement type="package" version="1.24.1">mothur</requirement>
  </requirements>
  <tests>
  </tests>