# HG changeset patch
# User artbio
# Date 1598435281 14400
# Node ID 49a8a327cc72549246261f917742c7fc486d7298
# Parent  41e68da5c0fe2b1e1a7c496327c55afd60355b7d
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit fa6b4f90ce05c65155b727e0eebaa27549621170"

diff -r 41e68da5c0fe -r 49a8a327cc72 lumpy_smoove.xml
--- 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 $prpos=="no":
     && sed -i -E 's/;PRPOS=.+\tGT/\tGT/g' output-smoove.vcf
diff -r 41e68da5c0fe -r 49a8a327cc72 macro_lumpy_smoove.xml
--- a/macro_lumpy_smoove.xml	Tue Aug 25 12:48:08 2020 -0400
+++ b/macro_lumpy_smoove.xml	Wed Aug 26 05:48:01 2020 -0400
@@ -6,8 +6,8 @@
         ln -s '${reference_source.ref_file}' reference.fa &&
         samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 &&
     #else:
-        ln -s '${source.index.fields.path}' reference.fa &&
-        ln -s '${source.index.fields.path}.fai' reference.fa.fai &&
+        ln -s '${reference_source.index.fields.path}' reference.fa &&
+        ln -s '${reference_source.index.fields.path}.fai' reference.fa.fai &&
     #end if
     ]]></token>