Mercurial > repos > bgruening > deeptools_alignmentsieve
comparison alignmentSieve.xml @ 2:ea8efdcf151f draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
| author | bgruening |
|---|---|
| date | Thu, 05 Apr 2018 10:57:35 -0400 |
| parents | dfc5a344e2c2 |
| children | d8c919d26d0e |
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| 1:48d08791d4f2 | 2:ea8efdcf151f |
|---|---|
| 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' |