Mercurial > repos > thanhlv > bin3c

diff mkmap.xml @ 17:1971cfa55ada draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bin3C commit 9f4ab03111185c7e20aaf669586278744713eee4
author thanhlv
date Mon, 21 Oct 2019 05:26:18 -0400
parents cdfc397e7b0f
children 327acdd0663d
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line diff
--- a/mkmap.xml	Thu Oct 17 12:41:47 2019 -0400
+++ b/mkmap.xml	Mon Oct 21 05:26:18 2019 -0400
@@ -6,6 +6,7 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
+        samtools sort -@ \${GALAXY_SLOTS:-1} -o sorted.bam -n $bam &&
         bin3C mkmap
         --min-extent $min_extent
         --min-reflen $min_reflen
@@ -22,7 +23,7 @@
                 -e $enzyme
             #end for 
         #end if
-        $ref $bam out
+        $ref sorted.bam out
     ]]></command>
     
     <inputs>