Mercurial > repos > trinity_ctat > align_and_estimate_abundance

changeset 13:321a69419c77 draft

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Changing alignment method to bowtie2
author trinity_ctat
date Thu, 28 Sep 2017 21:28:18 -0400
parents a130d5b5f34b
children 6e1eb00bfa53
files align_and_estimate_abundance.xml
diffstat 1 files changed, 3 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- 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":