# HG changeset patch
# User trinity_ctat
# Date 1506648498 14400
# Node ID 321a69419c77f8348c152e2602a1ee4d1a41af40
# Parent  a130d5b5f34b90ddb7983c7ce8a711ed7dddbd2b
Changing alignment method to bowtie2

diff -r a130d5b5f34b -r 321a69419c77 align_and_estimate_abundance.xml
--- a/align_and_estimate_abundance.xml	Tue Sep 26 23:11:20 2017 -0400
+++ b/align_and_estimate_abundance.xml	Thu Sep 28 21:28:18 2017 -0400
@@ -1,18 +1,16 @@
-<tool id="RSEM_abundance_estimation" name="align_and_estimate_abundance" version="2.0.0">
+<tool id="RSEM_abundance_estimation" name="align_and_estimate_abundance" version="1.0.0">
 
     <description>run RSEM to estimate transcript abundances</description>
 
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
+        <requirement type="package" version="1.3.0">rsem</requirement>
         <requirement type="package" version="2.4.0">trinity</requirement>
-        <requirement type="package">bowtie2</requirement>
-        <requirement type="package">samtools</requirement>
-        <requirement type="package">rsem</requirement>
     </requirements>
 
     <command>
         <![CDATA[
-        python $__tool_directory__/trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie --trinity_mode --prep_reference --output_dir  "subdir" 
+        python $__tool_directory__/trinityToolWrapper.py util/align_and_estimate_abundance.pl --transcripts $transcripts --est_method RSEM --aln_method bowtie2 --trinity_mode --prep_reference --output_dir  "subdir" 
 
         ## Inputs.
         #if str($inputs.paired_or_single) == "paired":