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

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

--- a/mothur/tools/mothur/pre.cluster.xml	Tue Jun 07 17:35:35 2011 -0400
+++ b/mothur/tools/mothur/pre.cluster.xml	Tue Jun 07 17:39:06 2011 -0400
@@ -1,16 +1,22 @@
-<tool id="mothur_pre_cluster" name="Pre.cluster" version="1.16.0">
+<tool id="mothur_pre_cluster" name="Pre.cluster" version="1.19.0">
  <description>Remove sequences due to pyrosequencing errors</description>
  <command interpreter="python">
   mothur_wrapper.py 
+  #import re, os.path
+  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
+  ## adds .precluster before the last extension to the input file
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.precluster.\2',$os.path.basename($fasta.__str__)) + ":'" + $fasta_out.__str__]
+  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.precluster.names',$os.path.basename($fasta.__str__)) + ":'" + $names_out.__str__]
   --cmd='pre.cluster'
-  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.precluster\.fasta$:'$fasta_out,'^\S+\.precluster\.names$:'$names_out
   --outputdir='$logfile.extra_files_path'
   --fasta=$fasta
-  #if $matrix.name.__str__ != "None" and len($matrix.name.__str__) > 0:
+  #if $name.__str__ != "None" and len($name.__str__) > 0:
    --name=$name
+  #end if
   #if 20 >= int($diffs.__str__) >= 0:
    --diffs=$diffs
   #end if
+  --result=#echo ','.join($results)
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Sequence Fasta"/>