Mercurial > repos > elixir-it > vinyl_optimizer

diff comando_galaxy_optimizer @ 2:6e4eb4856874 draft

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author elixir-it
date Wed, 22 Jul 2020 19:20:30 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/comando_galaxy_optimizer	Wed Jul 22 19:20:30 2020 +0000
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+ln -s /export/matteo_wrapper/optimizer/score_complete_alt.pl 2>/export/galaxy/database/files/000/dataset_586.dat && ln -s /export/matteo_wrapper/optimizer/wilcox.R 2>>/export/galaxy/database/files/000/dataset_586.dat &&     perl /export/matteo_wrapper/optimizer/optimizer.pl    -fileR /export/galaxy/database/files/000/dataset_576.dat -fileC /export/galaxy/database/files/000/dataset_577.dat     -leQTL /export/matteo_wrapper/optimizer/qfile     -keywords /export/matteo_wrapper/optimizer/kfile  -effects /export/matteo_wrapper/optimizer/efile   -disease_clinvar [4,6]  -score_AF [2,4]  -score_functional [4,6]  -score_NS [2,4]  -score_nIND [2,4]  -AF 0.0001  -scoreeQTL [2,4]   -scoreG [3,5]  -ofile /export/galaxy/database/files/000/dataset_587.dat  2>>/export/galaxy/database/files/000/dataset_586.dat
+
+perl optimizer.pl -leQTL qfile -similarD sfile -disease dilated_ -lgenes
+DCM_genes -fileR ALL_DCM_Final.vcf.annovar_ANNOT_B.hg19_multianno.vcf
+-fileC test_unaffected.vcf -ofile test_RES_2
+