Mercurial > repos > jjohnson > arriba

comparison arriba_download_reference.xml @ 4:77021ad5037d draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
author jjohnson
date Sat, 09 Oct 2021 15:41:49 +0000
parents 2d32e6c86c48
children 005b200c8841
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3:2d32e6c86c48 4:77021ad5037d
10 BASE_DIR=\$(dirname \$(dirname `which arriba`)) && 10 BASE_DIR=\$(dirname \$(dirname `which arriba`)) &&
11 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` && 11 REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` &&
12 \$REF_SCRIPT '$arriba_reference_name' && 12 \$REF_SCRIPT '$arriba_reference_name' &&
13 cp *.fa* '$genome_fasta' && 13 cp *.fa* '$genome_fasta' &&
14 cp *.gtf* '$genome_gtf' && 14 cp *.gtf* '$genome_gtf' &&
15 mv STAR*/* '$star_index.extra_files_path' 15 mv STAR_index_* '$star_index.extra_files_path'
16 ]]></command> 16 ]]></command>
17 <inputs> 17 <inputs>
18 <param name="arriba_reference_name" type="select" label="Select reference"> 18 <param name="arriba_reference_name" type="select" label="Select reference">
19 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option> 19 <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option>
20 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option> 20 <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option>