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comparison tepid-discover.xml @ 1:cea423bd0cd2 draft

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planemo upload for repository https://github.com/ListerLab/TEPID commit 40ee682fc4468bcdcc77f79a3bd098dc7f0019a7-dirty
author mvdbeek
date Thu, 05 Jan 2017 12:27:56 -0500
parents a5ef6470e54d
children 4a028613cfae
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0:a5ef6470e54d 1:cea423bd0cd2
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>tepid-discover --version</version_command> 7 <version_command>tepid-discover --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @LINK_CONC@ 9 @LINK_CONC@
10 tepid-discover 10 tepid-discover
11 -n '$split_bam.element_identifier'
11 $deletions 12 $deletions
12 $insertions 13 $insertions
13 $strict 14 $strict
14 #if $mask: 15 #if $mask:
15 --mask '$mask' 16 --mask '$mask'
18 --discordant '$discordant_bam' 19 --discordant '$discordant_bam'
19 #end if 20 #end if
20 @PROC@ 21 @PROC@
21 @NAME@ 22 @NAME@
22 -c conc.bam 23 -c conc.bam
23 -s '$split_bam' 24 -s split.bam
24 -t '$te_annotation_bed' 25 -t '$te_annotation_bed'
26 -k
25 $se_mode && ## The follwing is terrible, but from_work_dir cannot deal with variables 27 $se_mode && ## The follwing is terrible, but from_work_dir cannot deal with variables
26 mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' && 28 mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' &&
27 mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' && 29 mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' &&
28 mv insertion_reads_'$bowtie2_bam.element_identifier'.txt '$insertion_reads_out' && 30 mv insertion_reads_'$bowtie2_bam.element_identifier'.txt '$insertion_reads_out' &&
29 mv deletion_reads_'$bowtie2_bam.element_identifier'.txt '$deletion_reads_out' && 31 mv deletion_reads_'$bowtie2_bam.element_identifier'.txt '$deletion_reads_out' &&