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comparison repenrich2.xml @ 4:c5bb2f9af708 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 6b3b1194af0de793a1b4892c5973da835f5c0902
author artbio
date Sat, 20 Apr 2024 23:23:40 +0000
parents 0efb0ee6a7e9
children 08e50af788f7
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3:0efb0ee6a7e9 4:c5bb2f9af708
24 bowtie2-build --threads \${GALAXY_SLOTS:-4} -f $refGenomeSource.genome genome 1>/dev/null && 24 bowtie2-build --threads \${GALAXY_SLOTS:-4} -f $refGenomeSource.genome genome 1>/dev/null &&
25 ln -s -f '$refGenomeSource.genome' 'genome.fa' && 25 ln -s -f '$refGenomeSource.genome' 'genome.fa' &&
26 #set index_path = 'genome' 26 #set index_path = 'genome'
27 #else: 27 #else:
28 #set index_path = $refGenomeSource.genome.fields.path 28 #set index_path = $refGenomeSource.genome.fields.path
29 bowtie-inspect $index_path > genome.fa && 29 ln -s '${index_path}.fa' 'genome.fa' &&
30 #end if 30 #end if
31 31
32 python $__tool_directory__/RepEnrich2_setup.py 32 python $__tool_directory__/RepEnrich2_setup.py
33 --annotation_file '$repeatmasker' 33 --annotation_file '$repeatmasker'
34 --genomefasta 'genome.fa' 34 --genomefasta 'genome.fa'