diff mothur/tools/mothur/libshuff.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/libshuff.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/libshuff.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,21 +1,19 @@
-<tool id="mothur_libshuff" name="Libshuff" version="1.16.0">
+<tool id="mothur_libshuff" name="Libshuff" version="1.19.0">
  <description>Cramer-von Mises tests communities for the same structure</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='libshuff'
   --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.libshuff\.summary$:'$summary,'^\S+\.libshuff\.coverage$:'$coverage
   --outputdir='$logfile.extra_files_path'
-  --READ_cmd='read.dist'
-  #if $matrix.format == "column":
-   --READ_column=$matrix.dist
-   --READ_name=$matrix.name
-  #elif $matrix.format == "phylip":
-   --READ_phylip=$matrix.dist
+  --phylip=$dist
+  --group=$group
+  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
+    --groups=$groups
   #end if
-  --READ_group=$group
   #if len($iters.__str__) > 0:
    --iters=$iters
   #end if
+  $sim
   #if $form == "discrete":
    #if 1.0 >= float($form.step.__str__) > 0.0:
     --step=$form.step
@@ -26,22 +24,17 @@
   #end if
  </command>
  <inputs>
-  <conditional name="matrix">
-   <param name="format" type="select" label="Select a Distance Matrix Format" help="">
-    <option value="column">Pairwise Column Matrix</option>
-    <option value="phylip">Phylip Distance Matrix</option>
-   </param>
-   <when value="column">
-    <param name="dist" type="data" format="pair.dist" label="read.dist(column=) - Distance Matrix"/>
-    <param name="name" type="data" format="names" label="read.dist(name) - Sequences Name reference"/>
-   </when>
-   <when value="phylip">
-    <param name="dist" type="data" format="lower.dist,square.dist" label="read.dist(phylip=) - Distance Matrix"/>
-   </when>
-  </conditional>
-  <param name="group" type="data" format="groups" label="read.dist(group=) - Groups"/>
-  <!-- ? conditional - to hide complexity -->
+  <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
+  <param name="group" type="data" format="groups" label="group - Groups"/>
+  <param name="groups" type="select" label="groups - Groups to condider" multiple="true">
+   <options from_dataset="group">
+    <column name="name" index="1"/>
+    <column name="value" index="1"/>
+    <filter type="unique_value" name="unq_grp" column="1" />
+   </options>
+  </param>
   <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
+  <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" help=""/>
   <conditional name="form">
    <param name="form" type="select" label="form - Select a Clustering Method" help="">
     <option value="integral" selected="true">Integral</option>