Mercurial > repos > mvdbeek > bam_readtagger

changeset 17:777fd55e66ac draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit f28b0130760f515502b7858bd92adf948a942f39-dirty
author mvdbeek
date Mon, 03 Apr 2017 09:40:32 -0400
parents ffd8bf1b9ebc
children 8fef53971086
files deploy.sh findcluster.xml
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/findcluster.xml	Fri Mar 31 16:28:20 2017 -0400
+++ b/findcluster.xml	Mon Apr 03 09:40:32 2017 -0400
@@ -5,8 +5,10 @@
     </requirements>
     <version_command>findcluster --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
+        ln -f -s $input_path input.bam &&
+        ln -f -s $input.metadata.bam_index input.bam.bai &&
         findcluster
-        --input_path '$input'
+        --input_path input.bam
         #if $reference_fasta:
             --reference_fasta '$reference_fasta'
         #end if