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comparison halfdeep.xml @ 1:a53e299fe1cb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep commit 6a77207f883c3e7732b318968fe5f87a6762e24f
author iuc
date Thu, 12 Dec 2024 09:08:40 +0000
parents 607d5e33c4c2
children ab8373ba3830
comparison
equal deleted inserted replaced
0:607d5e33c4c2 1:a53e299fe1cb
28 echo 'reads/${reads_base}.$reads.ext' >> input.fofn && 28 echo 'reads/${reads_base}.$reads.ext' >> input.fofn &&
29 ## 29 ##
30 ## mapped reads 30 ## mapped reads
31 ## 31 ##
32 #if $mapped_reads 32 #if $mapped_reads
33 ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}.bam' && 33 ln -s '$mapped_reads' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.bam' &&
34 ln -s '${reads_base}.bam' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam' && 34 ln -s '${reads_base}${reads.ext}.bam' 'halfdeep/ref/mapped_reads/${reads_base}${reads.ext}.sort.bam' &&
35 ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}.sort.bam.bai' && 35 ln -s '$mapped_reads.metadata.bam_index' 'halfdeep/ref/mapped_reads/${reads_base}{reads.ext}.sort.bam.bai' &&
36 #end if 36 #end if
37 ## 37 ##
38 ## run bam_depth.sh 38 ## run bam_depth.sh
39 ## 39 ##
40 bam_depth.sh 'ref.$ref.ext' 1 && 40 bam_depth.sh 'ref.$ref.ext' 1 &&