diff mothur/tools/mothur/cluster.split.xml @ 2:e990ac8a0f58

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

--- a/mothur/tools/mothur/cluster.split.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/cluster.split.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,9 +1,9 @@
-<tool id="mothur_cluster_split" name="Cluster.split" version="1.16.0">
+<tool id="mothur_cluster_split" name="Cluster.split" version="1.19.0">
  <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='cluster.split'
-  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist
+  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist,'^\S+\.dist$:'$dist_out
   --outputdir='$logfile.extra_files_path'
   #if $splitby.splitmethod == "distance":
    #if $splitby.matrix.format == "column":
@@ -72,26 +72,26 @@
    <when value="classify">
     <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
     <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
-    <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
+    <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
     <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" 
            help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
    </when>
    <when value="fasta">
     <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
     <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
-    <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
+    <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/>
     <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" 
            help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/>
    </when>
   </conditional> <!-- splitby -->
   <param name="method" type="select" label="method - Select a Clustering Method" help="">
-   <option value="furthest" selected="true">Furthest neighbor</option>
+   <option value="furthest">Furthest neighbor</option>
    <option value="nearest">Nearest neighbor</option>
-   <option value="average">Average neighbor</option>
+   <option value="average" selected="true">Average neighbor</option>
   </param>
   <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" 
                  help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
-  <param name="hard" type="boolean" checked="false" truevalue="--hard=true" falsevalue="" label="hard - Use hard cutoff instead of rounding" 
+  <param name="hard" type="boolean" checked="true" truevalue="--hard=true" falsevalue="--hard=true" label="hard - Use hard cutoff instead of rounding" 
                  help=""/>
   <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
                  help="Set higher precision for longer genome scale sequence lengths">
@@ -110,6 +110,9 @@
   <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
   <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
   <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/>
+  <data format="pair.dist" name="dist_out" label="${tool.name} on ${on_string}: Column dist">
+   <filter>splitby.splitmethod == 'fasta' </filter>
+  </data>
  </outputs>
  <requirements>
   <requirement type="binary">mothur</requirement>