diff mothur/tools/mothur/tree.shared.xml @ 26:5c77423823cb

Updates for Mothur version 1.25.0 (includes changes to datatypes metagenomics.py and uses more efficient means for labels and groups options)

--- a/mothur/tools/mothur/tree.shared.xml	Wed May 16 12:28:44 2012 -0500
+++ b/mothur/tools/mothur/tree.shared.xml	Wed May 16 13:12:05 2012 -0500
@@ -1,4 +1,4 @@
-<tool id="mothur_tree_shared" name="Tree.shared" version="1.23.0" force_history_refresh="True">
+<tool id="mothur_tree_shared" name="Tree.shared" version="1.25.0" force_history_refresh="True">
  <description>Generate a newick tree for dissimilarity among groups</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -7,7 +7,7 @@
    --result='^mothur.\S+\.logfile$:'$logfile
    #if $input.as_datasets.__str__ == "yes":
     --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-    --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)\.tre)$:tre'
+    --new_datasets='^\S+?([a-z]+\.(unique|[0-9.]*)(\.(all|ave|cons))?\.tre)$:tre'
    #end if
    --shared=$input.dist
    #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
@@ -16,6 +16,16 @@
    #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
     --label='$input.label'
    #end if
+   #if $input.subsampling.use:
+    #if len($input.subsampling.subsample.__str__) > 0 and int($input.subsampling.subsample.__str__) > 0:
+     --subsample=$input.subsampling.subsample
+    #else
+     --subsample=T
+    #end if
+    #if len($input.subsampling.iters.__str__) > 0 and int($input.subsampling.iters.__str__) > 0:
+     --iters=$input.subsampling.iters
+    #end if
+   #end if
   #else: 
    --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.tre$:'$tre
    --outputdir='$logfile.extra_files_path'
@@ -32,6 +42,7 @@
   #if $calc.__str__ != "None" and len($calc.__str__) > 0:
    --calc=$calc
   #end if
+  --processors=8
  </command>
  <inputs>
   <!-- column,name  phylip  or shared -->
@@ -62,6 +73,17 @@
        <filter type="data_meta" ref="dist" key="groups" />
       </options>
      </param>
+     <conditional name="subsampling">
+      <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="subsample"/>
+      <when value="yes">
+       <param name="subsample" type="integer" value="" optional="true" label="subsample (defaults to the size of the smallest group)"
+              help="Should not exceed the number of sequences in any group"/>
+       <param name="iters" type="integer" value="" optional="true" label="iters - Number of iterations to try (default 1000)">
+         <validator type="in_range" message="Number of iterations must be positive" min="1"/>
+       </param>
+      </when>
+      <when value="no"/>
+     </conditional> <!-- subsampling -->
    </when>
   </conditional>
   <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">