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comparison repenrich.xml @ 15:2e3d976e7d5d draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 03183e29f807ec33548016a7c4144f52720b7b9e
author artbio
date Sun, 21 Apr 2024 09:44:51 +0000
parents 530626b0757c
children
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14:bf866bedd4b4 15:2e3d976e7d5d
32 ln -f -s '$seq_method.input_fastq' 'input.fastq' && 32 ln -f -s '$seq_method.input_fastq' 'input.fastq' &&
33 ln -f -s '$seq_method.input2_fastq' 'input_2.fastq' && 33 ln -f -s '$seq_method.input2_fastq' 'input_2.fastq' &&
34 #end if 34 #end if
35 #end if 35 #end if
36 ln -f -s '$genome' 'genome.fa' && 36 ln -f -s '$genome' 'genome.fa' &&
37 bowtie-build '$genome' genome && 37 bowtie-build --threads \${GALAXY_SLOTS:-1} '$genome' genome &&
38 python $__tool_directory__/RepEnrich_setup.py 38 python $__tool_directory__/RepEnrich_setup.py
39 --annotation_file '$repeatmasker' 39 --annotation_file '$repeatmasker'
40 --genomefasta 'genome.fa' 40 --genomefasta 'genome.fa'
41 --cpus "\${GALAXY_SLOTS:-4}" && 41 --cpus "\${GALAXY_SLOTS:-4}" &&
42 #if $seq_method.seq_method_list == "single-read": 42 #if $seq_method.seq_method_list == "single-read":