Mercurial > repos > iuc > jvarkit_wgscoverageplotter

comparison jvarkit_wgscoverageplotter.xml @ 3:1eac3ae5d8c7 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit 7224953c0b42f43a91dc76ee1015f355a311b391"
author iuc
date Fri, 12 Feb 2021 12:54:29 +0000
parents cf2d9bf2d7ad
children
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2:964c6f212043 3:1eac3ae5d8c7
23 #end if 23 #end if
24 samtools view -H '$alignment_file' |grep -E '^(@HD|@SQ)' >reference.dict && 24 samtools view -H '$alignment_file' |grep -E '^(@HD|@SQ)' >reference.dict &&
25 cat reference.dict && 25 cat reference.dict &&
26 ln -s '$alignment_file' '$alignment_name' && 26 ln -s '$alignment_file' '$alignment_name' &&
27 ln -s '${alignment_file.metadata.bam_index}' '${alignment_name}.bai' && 27 ln -s '${alignment_file.metadata.bam_index}' '${alignment_name}.bai' &&
28 wgscoverageplotter.sh 28 wgscoverageplotter.py
29 --reference reference.fasta 29 --reference reference.fasta
30 --dimension '$dimension' 30 --dimension '$dimension'
31 --output plot.svg 31 --output plot.svg
32 $adv.disable_paired_overlap 32 $adv.disable_paired_overlap
33 #if $include_regex 33 #if $include_regex