Mercurial > repos > bgruening > deeptools_alignmentsieve

comparison alignmentSieve.xml @ 2:28b2aa3ac6a6 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
author bgruening
date Thu, 05 Apr 2018 10:44:59 -0400
parents 0d0b4fb6eec2
children 5e3816edfd1b
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equal deleted inserted replaced
1:337cef30697f 2:28b2aa3ac6a6
73 --ATACshift 73 --ATACshift
74 #end if 74 #end if
75 #if $BED: 75 #if $BED:
76 --BED 76 --BED
77 -o '$outFile' 77 -o '$outFile'
78 #elif str($shift) != "": 78 #elif str($shift) != "" or $ATACshift:
79 -o foo.bam && 79 -o foo.bam &&
80 samtools sort -o '$outFile' -T foo.tmp -@ "\${GALAXY_SLOTS:-4}" foo.bam && 80 samtools sort -o '$outFile' -T foo.tmp -@ "\${GALAXY_SLOTS:-4}" foo.bam &&
81 rm foo.bam 81 rm foo.bam
82 #else: 82 #else:
83 -o '$outFile' 83 -o '$outFile'