Mercurial > repos > mvdbeek > tepid_discover

comparison tepid-discover.xml @ 3:370c325b5941 draft

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planemo upload for repository https://github.com/ListerLab/TEPID commit 48d24b91382cfbe7749d131657efbad47a28f569-dirty
author mvdbeek
date Fri, 06 Jan 2017 08:06:16 -0500
parents 4a028613cfae
children df634cd04be7
comparison
equal deleted inserted replaced
2:4a028613cfae 3:370c325b5941
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 '$insertions_out' && 28 #if not str($deletions)=="--deletions":
29 mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' && 29 mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' &&
30 mv insertion_reads_'$bowtie2_bam.element_identifier'.txt '$insertion_reads_out' && 30 mv insertion_reads_'$bowtie2_bam.element_identifier'.txt '$insertion_reads_out' &&
31 mv deletion_reads_'$bowtie2_bam.element_identifier'.txt '$deletion_reads_out' && 31 #end if
32 #if not str($insertions)=="--insertions":
33 mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' &&
34 mv deletion_reads_'$bowtie2_bam.element_identifier'.txt '$deletion_reads_out' &&
35 #end if
32 cat tepid_discover_log_'$bowtie2_bam.element_identifier'.txt 36 cat tepid_discover_log_'$bowtie2_bam.element_identifier'.txt
33 ]]></command> 37 ]]></command>
34 <inputs> 38 <inputs>
35 <param name="bowtie2_bam" label="Alignment file (Bowtie2)" argument="--conc" type="data" format="bam"/> 39 <param name="bowtie2_bam" label="Alignment file (Bowtie2)" argument="--conc" type="data" format="bam"/>
36 <param name="discordant_bam" label="Alignment file with discordant pairs" argument="--discordant" optional="true" type="data" format="bam"/> 40 <param name="discordant_bam" label="Alignment file with discordant pairs" argument="--discordant" optional="true" type="data" format="bam"/>