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comparison tepid-discover.xml @ 2:4a028613cfae draft

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planemo upload for repository https://github.com/ListerLab/TEPID commit 40ee682fc4468bcdcc77f79a3bd098dc7f0019a7-dirty
author mvdbeek
date Thu, 05 Jan 2017 12:57:26 -0500
parents cea423bd0cd2
children 370c325b5941
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1:cea423bd0cd2 2:4a028613cfae
19 --discordant '$discordant_bam' 19 --discordant '$discordant_bam'
20 #end if 20 #end if
21 @PROC@ 21 @PROC@
22 @NAME@ 22 @NAME@
23 -c conc.bam 23 -c conc.bam
24 -s split.bam 24 -s '$split_bam'
25 -t '$te_annotation_bed' 25 -t '$te_annotation_bed'
26 -k 26 -k
27 $se_mode && ## The follwing is terrible, but from_work_dir cannot deal with variables 27 $se_mode && ## The follwing is terrible, but from_work_dir cannot deal with variables
28 mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' && 28 mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' &&
29 mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' && 29 mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' &&