Mercurial > repos > artbio > lumpy_smoove
comparison macro_lumpy_smoove.xml @ 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 | ee8fc44b1655 |
children |
comparison
equal
deleted
inserted
replaced
1:41e68da5c0fe | 2:49a8a327cc72 |
---|---|
4 <token name="@set_fasta_index@"><![CDATA[ | 4 <token name="@set_fasta_index@"><![CDATA[ |
5 #if str( $reference_source.reference_source_selector ) == "history": | 5 #if str( $reference_source.reference_source_selector ) == "history": |
6 ln -s '${reference_source.ref_file}' reference.fa && | 6 ln -s '${reference_source.ref_file}' reference.fa && |
7 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 && | 7 samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for lumpy_smoove" >&2 && |
8 #else: | 8 #else: |
9 ln -s '${source.index.fields.path}' reference.fa && | 9 ln -s '${reference_source.index.fields.path}' reference.fa && |
10 ln -s '${source.index.fields.path}.fai' reference.fa.fai && | 10 ln -s '${reference_source.index.fields.path}.fai' reference.fa.fai && |
11 #end if | 11 #end if |
12 ]]></token> | 12 ]]></token> |
13 | 13 |
14 <macro name="reference_source_conditional"> | 14 <macro name="reference_source_conditional"> |
15 <conditional name="reference_source"> | 15 <conditional name="reference_source"> |