Mercurial > repos > yating-l > bamtobigwig

changeset 2:f7f035d9d48a draft default tip

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planemo upload commit 250051c3d660df43da92c76913552767ce142a45-dirty
author yating-l
date Tue, 30 May 2017 18:01:45 -0400
parents 87341e6002eb
children
files bam_to_bigwig.xml
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/bam_to_bigwig.xml	Tue Feb 07 17:09:08 2017 -0500
+++ b/bam_to_bigwig.xml	Tue May 30 18:01:45 2017 -0400
@@ -9,7 +9,9 @@
     <command><![CDATA[
         faToTwoBit $input_reference_fasta two_bit.2bit;
         twoBitInfo two_bit.2bit stdout | sort -k2nr > chrom.sizes;
-        bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes > temp.bg;
+        bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes 
+        | LC_COLLATE=C sort -k1,1 -k2,2n
+        > temp.bg &&
         bedGraphToBigWig temp.bg chrom.sizes $output_bigwig;
     ]]></command>
     <inputs>