diff mothur/tools/mothur/cluster.fragments.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

--- a/mothur/tools/mothur/cluster.fragments.xml	Tue Jun 07 17:32:23 2011 -0400
+++ b/mothur/tools/mothur/cluster.fragments.xml	Tue Jun 07 17:35:35 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.15.0">
+<tool id="mothur_cluster_fragments" name="Cluster.fragments" version="1.16.0">
  <description> Group sequences that are part of a larger sequence</description>
  <command interpreter="python">
   mothur_wrapper.py 
@@ -7,10 +7,21 @@
   --outputdir='$logfile.extra_files_path'
   --fasta=$fasta
   --name=$names
+  #if int($diffs.__str__) > 0:
+   --diffs=$diffs
+  #end if
+  #if 100 >= int($percent.__str__) > 0:
+   --percent=$percent
+  #end if
  </command>
  <inputs>
   <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
   <param name="names" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
+  <param name="diffs" type="integer" value="0" label="diffs - Number of mismatched bases to allow between sequences in a group (default 0)"/>
+  <param name="percent" type="integer" value="0" label="percent - percentage of differences allowed ( between 1 and 100, default 0)" 
+    help="The percent parameter allows you to set percentage of differences allowed, default=0. percent=2 means if the number of difference is less than or equal to two percent of the length of the fragment, then cluster. You may use diffs and percent at the same time to say something like: If the number or differences is greater than 1 or more than 2% of the fragment length, don't merge.">
+   <validator type="in_range" message="percentage differences allowed  must be between 0 and 100" min="0" max="100"/>
+  </param>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />