Mercurial > repos > artbio > lumpy_smoove

diff lumpy_smoove.xml @ 2:49a8a327cc72 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit fa6b4f90ce05c65155b727e0eebaa27549621170"
author artbio
date Wed, 26 Aug 2020 05:48:01 -0400
parents ee8fc44b1655
children 65b400409455
line wrap: on
line diff
--- a/lumpy_smoove.xml	Tue Aug 25 12:48:08 2020 -0400
+++ b/lumpy_smoove.xml	Wed Aug 26 05:48:01 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="lumpy_smoove" name="lumpy_smoove" version="0.2.0">
+<tool id="lumpy_smoove" name="lumpy_smoove" version="0.4.0">
     <description>find structural variants using the smoove workflow</description>
     <macros>
         <import>macro_lumpy_smoove.xml</import>
@@ -19,7 +19,7 @@
         #if $set_exclusion.choices=="yes":
             --exclude $bedmask
         #end if
-        --fasta reference.fa -p 24 normal.bam tumor.bam &&
+        --fasta reference.fa -p \${GALAXY_SLOTS:-4} normal.bam tumor.bam &&
     gunzip output-smoove.vcf.gz
     #if $prpos=="no":
     && sed -i -E 's/;PRPOS=.+\tGT/\tGT/g' output-smoove.vcf