Mercurial > repos > ebi-gxa > gtf2gene_list

annotate gtf2gene.R @ 0:040d4b3a19d5 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 12:05:26 -0400
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040d4b3a19d5 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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1 #!/usr/bin/env Rscript
040d4b3a19d5 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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2
040d4b3a19d5 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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3 suppressPackageStartupMessages(require(rtracklayer))
040d4b3a19d5 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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4 args <- commandArgs(TRUE)
040d4b3a19d5 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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5
040d4b3a19d5 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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6 annotation <- elementMetadata(import( args[1] ))
040d4b3a19d5 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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7 genes <- unique(annotation[['gene_id']])
040d4b3a19d5 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 9bf9a6e46a330890be932f60d1d996dd166426c4
ebi-gxa
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8 writeLines(genes[ ! is.na(genes)], con = 'genes.txt')