Mercurial > repos > artbio > lumpy_smoove
changeset 2:49a8a327cc72 draft
"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 | 41e68da5c0fe |
| children | 65b400409455 |
| files | lumpy_smoove.xml macro_lumpy_smoove.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- 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 $prpos=="no": && sed -i -E 's/;PRPOS=.+\tGT/\tGT/g' output-smoove.vcf
--- a/macro_lumpy_smoove.xml Tue Aug 25 12:48:08 2020 -0400 +++ b/macro_lumpy_smoove.xml Wed Aug 26 05:48:01 2020 -0400 @@ -6,8 +6,8 @@ ln -s '${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>