Mercurial > repos > jjohnson > arriba
comparison arriba_download_reference.xml @ 3:2d32e6c86c48 draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
author | jjohnson |
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date | Fri, 08 Oct 2021 20:44:25 +0000 |
parents | 7420753b0671 |
children | 77021ad5037d |
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2:7420753b0671 | 3:2d32e6c86c48 |
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8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 echo $arriba_reference_name > '$star_index' && | 9 echo $arriba_reference_name > '$star_index' && |
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*/* '$star_index.extra_files_path' | 15 mv STAR*/* '$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> |