Mercurial > repos > jjohnson > arriba

comparison arriba_download_reference.xml @ 3:2d32e6c86c48 draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"
author jjohnson
date Fri, 08 Oct 2021 20:44:25 +0000
parents 7420753b0671
children 77021ad5037d
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2:7420753b0671 3:2d32e6c86c48
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>