comparison convertMAF.sh @ 57:94264fe60478 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 4b5df41484f6bdf316edaf95b53c92d328ec1674-dirty

56:c0097a584a8a

#!/usr/bin/env bash
# https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
#  MAF file must contain the species name and chromosome name
#  e.g. hg38.chr1 in the sequence identifiers.
perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
bgzip $4.sorted.bed
tabix -p bed $4.sorted.bed.gz

57:94264fe60478

#!/usr/bin/env bash
# https://github.com/cmdcolin/jbrowse-plugin-mafviewer/blob/master/bin/convert.sh
#  MAF file must contain the species name and chromosome name
#  e.g. hg38.chr1 in the sequence identifiers.
perl $3/maf2bed.pl $2 < $1 | sort -k1,1 -k2,2n > $4.sorted.bed
bgzip -c $4.sorted.bed > $4.sorted.bed.gz
tabix -p bed $4.sorted.bed.gz