# HG changeset patch # User iuc # Date 1584695477 14400 # Node ID 0170de5072d4417a492d7e0e4babafc3db4b3cb9 # Parent c96f1a93beb77a3a2ad628f0bb7d0ceef598dd89 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086" diff -r c96f1a93beb7 -r 0170de5072d4 chira_merge.xml --- a/chira_merge.xml Thu Mar 12 17:05:50 2020 -0400 +++ b/chira_merge.xml Fri Mar 20 05:11:17 2020 -0400 @@ -9,9 +9,17 @@ -b '$alignments' #if str($annotation.choice) == "yes": -g '$annotation.gtf' - #end if - -ao '$alignment_overlap' + #end if -so '$segment_overlap' + #if str($merge.mode) == "blockbuster": + -bb + -d '$merge.distance' + -mc '$merge.min_cluster_height' + -mb '$merge.min_block_height' + -sc '$merge.scale' + #else: + -ao '$merge.alignment_overlap' + #end if -o ./ ]]> @@ -27,12 +35,30 @@ - + - + + + + + + + + + + + + + + + @@ -40,34 +66,54 @@ - + - + - + + - + - + - + + + + + + + + + + + + + + + + + + + + diff -r c96f1a93beb7 -r 0170de5072d4 macros.xml --- a/macros.xml Thu Mar 12 17:05:50 2020 -0400 +++ b/macros.xml Fri Mar 20 05:11:17 2020 -0400 @@ -1,6 +1,6 @@ @TOOL_VERSION@+galaxy - 1.0.4 + 1.1.2 chira diff -r c96f1a93beb7 -r 0170de5072d4 test-data/alignments.bed --- a/test-data/alignments.bed Thu Mar 12 17:05:50 2020 -0400 +++ b/test-data/alignments.bed Fri Mar 20 05:11:17 2020 -0400 @@ -1,337 +1,337 @@ -mmu-miR-124-3p 0 20 3|2,mmu-miR-124-3p,0,20,+,5S20M30S 0 + -ENSMUST00000182884 6023 6051 28|3,ENSMUST00000182884,6023,6051,+,27S28M 0 + -ENSMUST00000182010 428 477 36|10,ENSMUST00000182010,428,477,+,5S49M1S 0 + -ENSMUST00000113560 1969 1992 38|2,ENSMUST00000113560,1969,1992,+,32S23M 0 + -mmu-miR-9-5p 0 23 11|1,mmu-miR-9-5p,0,23,+,5S23M27S 0 + -mmu-miR-9-5p 0 23 38|2,mmu-miR-9-5p,0,23,+,5S23M27S 0 + -ENSMUST00000138581 1621 1644 38|2,ENSMUST00000138581,1621,1644,+,32S23M 0 + -ENSMUST00000182010 419 468 34|1,ENSMUST00000182010,419,468,+,5S49M1S 0 + -ENSMUST00000047061 2204 2232 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test-data/segments.bed --- a/test-data/segments.bed Thu Mar 12 17:05:50 2020 -0400 +++ b/test-data/segments.bed Fri Mar 20 05:11:17 2020 -0400 @@ -1,13 +1,13 @@ -ENSMUST00000182010 19 68 6|1|1,ENSMUST00000182010,19,68,+,5S49M1S 0 + -ENSMUST00000182010 24 74 7|9|1,ENSMUST00000182010,24,74,+,5S50M 0 + -mmu-miR-20a-5p 0 23 3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S 0 + -mmu-miR-6898-5p 11 21 2|2|1,mmu-miR-6898-5p,11,21,+,10M39S 0 + -mmu-miR-6979-3p 2 12 4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S 0 + -ENSMUST00000137264 12 27 2|2|2,ENSMUST00000137264,12,27,+,4S15M30S 0 + -ENSMUST00000136025 32 46 4|1|2,ENSMUST00000136025,32,46,+,1S14M39S 0 + -ENSMUST00000136025 132 142 3|2|2,ENSMUST00000136025,132,142,+,34S10M11S 0 + -ENSMUST00000182010 19 45 6|1|2,ENSMUST00000182010,19,45,+,5S26M24S 0 + -ENSMUST00000182010 24 45 7|9|2,ENSMUST00000182010,24,45,+,5S21M29S 0 + -ENSMUST00000182010 46 58 6|1|3,ENSMUST00000182010,46,58,+,32S12M11S 0 + -ENSMUST00000182010 46 68 7|9|3,ENSMUST00000182010,46,68,+,27S22M6S 0 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