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diff cd_hit_est.xml @ 2:cca0838c1597

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Add an environment variable for the -M and -T options for memory and thread allocation
author Jim Johnson <jj@umn.edu>
date Tue, 26 Feb 2013 12:11:36 -0600
parents 34a799d173f7
children 43724ea1c85f
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--- a/cd_hit_est.xml	Fri Sep 07 13:52:03 2012 -0500
+++ b/cd_hit_est.xml	Tue Feb 26 12:11:36 2013 -0600
@@ -1,10 +1,10 @@
-<tool id="cd_hit_est" name="CD-HIT-EST" version="1.1">
+<tool id="cd_hit_est" name="CD-HIT-EST" version="1.2">
  <description>Cluster a nucleotide dataset into representative sequences</description>
  <requirements>
   <requirement type="package" version="4.6.1">cd-hit</requirement>
  </requirements>
  <command>
-  cd-hit-est -i $fasta_in -o rep_seq -c $similarity -n $wordsize $strand
+  cd-hit-est \$CDHIT_SITE_OPTIONS -i "$fasta_in" -o rep_seq -c $similarity -n $wordsize $strand
  </command>
  <inputs>
   <param name="fasta_in" type="data" format="fasta" label="EST Sequences to cluster"/>