Mercurial > repos > artbio > lumpy_smoove

comparison macro_lumpy_smoove.xml @ 2:49a8a327cc72 draft

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"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
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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">