# HG changeset patch # User bgruening # Date 1685615028 0 # Node ID 0d2ba04b8261afad8a7280403b5898aa9a2c69f4 # Parent a4ecef241a6da4722481f4e69e6f710decc6d1d9 planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9 diff -r a4ecef241a6d -r 0d2ba04b8261 bamCoverage.xml --- a/bamCoverage.xml Fri Feb 11 10:46:30 2022 +0000 +++ b/bamCoverage.xml Thu Jun 01 10:23:48 2023 +0000 @@ -1,4 +1,4 @@ - + generates a coverage bigWig file from a given BAM or CRAM file bamCoverage diff -r a4ecef241a6d -r 0d2ba04b8261 deepTools_macros.xml --- a/deepTools_macros.xml Fri Feb 11 10:46:30 2022 +0000 +++ b/deepTools_macros.xml Thu Jun 01 10:23:48 2023 +0000 @@ -1,10 +1,11 @@ --numberOfProcessors "\${GALAXY_SLOTS:-4}" - 3.5.1.0 + 3.5.2 + 20.01 - deeptools + deeptools samtools @@ -368,7 +369,6 @@ - .. class:: infomark @@ -483,7 +483,7 @@ `__. For bug reports and feature requests please open an issue ``__. - - -============ -Installation -============ - -Requirements: python-2.7 - -Galaxy should be able to automatically install all other dependencies, such as numpy or scipy. - -For the best performance we recommend to install blas/lapack/atlas in your environment before -installing deepTools from the Tool Shed. - - -======== -Citation -======== - -deeptools are currently under review. In the meantime please refere to https://github.com/deeptools/deepTools. - - -======= -History -======= - - * v1.0: Initial public release - * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version - - -Licence (MIT) -============= - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. diff -r a4ecef241a6d -r 0d2ba04b8261 repository_dependencies.xml --- a/repository_dependencies.xml Fri Feb 11 10:46:30 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - \ No newline at end of file diff -r a4ecef241a6d -r 0d2ba04b8261 test-data/bigwigAverage2.bw Binary file test-data/bigwigAverage2.bw has changed diff -r a4ecef241a6d -r 0d2ba04b8261 test-data/multiBigwigSummary_result1.npz Binary file test-data/multiBigwigSummary_result1.npz has changed diff -r a4ecef241a6d -r 0d2ba04b8261 test-data/multiBigwigSummary_result2.npz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiBigwigSummary_result2.npz Thu Jun 01 10:23:48 2023 +0000 @@ -0,0 +1,121 @@ +#'chr' 'start' 'end' 'sample1' 'sample2' +ch1 0 10 0.0 0.0 +ch1 10 20 0.0 0.0 +ch1 20 30 0.0 0.0 +ch1 30 40 0.0 0.0 +ch1 40 50 0.0 0.0 +ch1 50 60 0.0 0.0 +ch1 60 70 0.0 0.0 +ch1 70 80 0.0 0.0 +ch1 80 90 0.0 0.0 +ch1 90 100 0.0 0.0 +ch1 100 110 2.0 2.0 +ch1 110 120 2.0 2.0 +ch1 120 130 1.0 1.0 +ch1 130 140 0.0 0.0 +ch1 140 150 0.0 0.0 +ch1 150 160 0.0 0.0 +ch1 160 170 0.0 0.0 +ch1 170 180 0.0 0.0 +ch1 180 190 0.0 0.0 +ch1 190 200 0.0 0.0 +ch1 200 210 0.0 0.0 +ch1 210 220 0.0 0.0 +ch1 220 230 0.0 0.0 +ch1 230 240 0.0 0.0 +ch1 240 250 0.0 0.0 +ch1 250 260 0.0 0.0 +ch1 260 270 0.0 0.0 +ch1 270 280 0.0 0.0 +ch1 280 290 0.0 0.0 +ch1 290 300 0.0 0.0 +ch1 300 310 0.0 0.0 +ch1 310 320 0.0 0.0 +ch1 320 330 0.0 0.0 +ch1 330 340 0.0 0.0 +ch1 340 350 0.0 0.0 +ch1 350 360 0.0 0.0 +ch1 360 370 0.0 0.0 +ch1 370 380 0.0 0.0 +ch1 380 390 0.0 0.0 +ch1 390 400 0.0 0.0 +ch2 0 10 0.0 0.0 +ch2 10 20 0.0 0.0 +ch2 20 30 0.0 0.0 +ch2 30 40 0.0 0.0 +ch2 40 50 0.0 0.0 +ch2 50 60 3.0 3.0 +ch2 60 70 3.0 3.0 +ch2 70 80 1.5 1.5 +ch2 80 90 0.0 0.0 +ch2 90 100 0.0 0.0 +ch2 100 110 0.0 0.0 +ch2 110 120 0.0 0.0 +ch2 120 130 0.0 0.0 +ch2 130 140 0.0 0.0 +ch2 140 150 0.0 0.0 +ch2 150 160 1.0 1.0 +ch2 160 170 1.0 1.0 +ch2 170 180 0.5 0.5 +ch2 180 190 0.0 0.0 +ch2 190 200 0.0 0.0 +ch2 200 210 0.0 0.0 +ch2 210 220 0.0 0.0 +ch2 220 230 0.0 0.0 +ch2 230 240 0.0 0.0 +ch2 240 250 0.0 0.0 +ch2 250 260 0.0 0.0 +ch2 260 270 0.0 0.0 +ch2 270 280 0.0 0.0 +ch2 280 290 0.0 0.0 +ch2 290 300 0.0 0.0 +ch2 300 310 0.0 0.0 +ch2 310 320 0.0 0.0 +ch2 320 330 0.0 0.0 +ch2 330 340 0.0 0.0 +ch2 340 350 0.0 0.0 +ch2 350 360 0.0 0.0 +ch2 360 370 0.0 0.0 +ch2 370 380 0.0 0.0 +ch2 380 390 0.0 0.0 +ch2 390 400 0.0 0.0 +ch3 0 10 0.0 0.0 +ch3 10 20 0.0 0.0 +ch3 20 30 0.0 0.0 +ch3 30 40 0.0 0.0 +ch3 40 50 0.0 0.0 +ch3 50 60 3.0 3.0 +ch3 60 70 3.0 3.0 +ch3 70 80 1.5 1.5 +ch3 80 90 0.0 0.0 +ch3 90 100 0.0 0.0 +ch3 100 110 0.0 0.0 +ch3 110 120 0.0 0.0 +ch3 120 130 0.0 0.0 +ch3 130 140 0.0 0.0 +ch3 140 150 0.0 0.0 +ch3 150 160 1.0 1.0 +ch3 160 170 1.0 1.0 +ch3 170 180 0.5 0.5 +ch3 180 190 0.0 0.0 +ch3 190 200 0.0 0.0 +ch3 200 210 0.0 0.0 +ch3 210 220 0.0 0.0 +ch3 220 230 0.0 0.0 +ch3 230 240 0.0 0.0 +ch3 240 250 0.0 0.0 +ch3 250 260 0.0 0.0 +ch3 260 270 0.0 0.0 +ch3 270 280 0.0 0.0 +ch3 280 290 0.0 0.0 +ch3 290 300 0.0 0.0 +ch3 300 310 0.0 0.0 +ch3 310 320 0.0 0.0 +ch3 320 330 0.0 0.0 +ch3 330 340 0.0 0.0 +ch3 340 350 0.0 0.0 +ch3 350 360 0.0 0.0 +ch3 360 370 0.0 0.0 +ch3 370 380 0.0 0.0 +ch3 380 390 0.0 0.0 +ch3 390 400 0.0 0.0 diff -r a4ecef241a6d -r 0d2ba04b8261 test-data/multiBigwigSummary_result2.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiBigwigSummary_result2.tabular Thu Jun 01 10:23:48 2023 +0000 @@ -0,0 +1,121 @@ +#'chr' 'start' 'end' 'sample1' 'sample2' +ch1 0 10 0.0 0.0 +ch1 10 20 0.0 0.0 +ch1 20 30 0.0 0.0 +ch1 30 40 0.0 0.0 +ch1 40 50 0.0 0.0 +ch1 50 60 0.0 0.0 +ch1 60 70 0.0 0.0 +ch1 70 80 0.0 0.0 +ch1 80 90 0.0 0.0 +ch1 90 100 0.0 0.0 +ch1 100 110 2.0 2.0 +ch1 110 120 2.0 2.0 +ch1 120 130 1.0 1.0 +ch1 130 140 0.0 0.0 +ch1 140 150 0.0 0.0 +ch1 150 160 0.0 0.0 +ch1 160 170 0.0 0.0 +ch1 170 180 0.0 0.0 +ch1 180 190 0.0 0.0 +ch1 190 200 0.0 0.0 +ch1 200 210 0.0 0.0 +ch1 210 220 0.0 0.0 +ch1 220 230 0.0 0.0 +ch1 230 240 0.0 0.0 +ch1 240 250 0.0 0.0 +ch1 250 260 0.0 0.0 +ch1 260 270 0.0 0.0 +ch1 270 280 0.0 0.0 +ch1 280 290 0.0 0.0 +ch1 290 300 0.0 0.0 +ch1 300 310 0.0 0.0 +ch1 310 320 0.0 0.0 +ch1 320 330 0.0 0.0 +ch1 330 340 0.0 0.0 +ch1 340 350 0.0 0.0 +ch1 350 360 0.0 0.0 +ch1 360 370 0.0 0.0 +ch1 370 380 0.0 0.0 +ch1 380 390 0.0 0.0 +ch1 390 400 0.0 0.0 +ch2 0 10 0.0 0.0 +ch2 10 20 0.0 0.0 +ch2 20 30 0.0 0.0 +ch2 30 40 0.0 0.0 +ch2 40 50 0.0 0.0 +ch2 50 60 3.0 3.0 +ch2 60 70 3.0 3.0 +ch2 70 80 1.5 1.5 +ch2 80 90 0.0 0.0 +ch2 90 100 0.0 0.0 +ch2 100 110 0.0 0.0 +ch2 110 120 0.0 0.0 +ch2 120 130 0.0 0.0 +ch2 130 140 0.0 0.0 +ch2 140 150 0.0 0.0 +ch2 150 160 1.0 1.0 +ch2 160 170 1.0 1.0 +ch2 170 180 0.5 0.5 +ch2 180 190 0.0 0.0 +ch2 190 200 0.0 0.0 +ch2 200 210 0.0 0.0 +ch2 210 220 0.0 0.0 +ch2 220 230 0.0 0.0 +ch2 230 240 0.0 0.0 +ch2 240 250 0.0 0.0 +ch2 250 260 0.0 0.0 +ch2 260 270 0.0 0.0 +ch2 270 280 0.0 0.0 +ch2 280 290 0.0 0.0 +ch2 290 300 0.0 0.0 +ch2 300 310 0.0 0.0 +ch2 310 320 0.0 0.0 +ch2 320 330 0.0 0.0 +ch2 330 340 0.0 0.0 +ch2 340 350 0.0 0.0 +ch2 350 360 0.0 0.0 +ch2 360 370 0.0 0.0 +ch2 370 380 0.0 0.0 +ch2 380 390 0.0 0.0 +ch2 390 400 0.0 0.0 +ch3 0 10 0.0 0.0 +ch3 10 20 0.0 0.0 +ch3 20 30 0.0 0.0 +ch3 30 40 0.0 0.0 +ch3 40 50 0.0 0.0 +ch3 50 60 3.0 3.0 +ch3 60 70 3.0 3.0 +ch3 70 80 1.5 1.5 +ch3 80 90 0.0 0.0 +ch3 90 100 0.0 0.0 +ch3 100 110 0.0 0.0 +ch3 110 120 0.0 0.0 +ch3 120 130 0.0 0.0 +ch3 130 140 0.0 0.0 +ch3 140 150 0.0 0.0 +ch3 150 160 1.0 1.0 +ch3 160 170 1.0 1.0 +ch3 170 180 0.5 0.5 +ch3 180 190 0.0 0.0 +ch3 190 200 0.0 0.0 +ch3 200 210 0.0 0.0 +ch3 210 220 0.0 0.0 +ch3 220 230 0.0 0.0 +ch3 230 240 0.0 0.0 +ch3 240 250 0.0 0.0 +ch3 250 260 0.0 0.0 +ch3 260 270 0.0 0.0 +ch3 270 280 0.0 0.0 +ch3 280 290 0.0 0.0 +ch3 290 300 0.0 0.0 +ch3 300 310 0.0 0.0 +ch3 310 320 0.0 0.0 +ch3 320 330 0.0 0.0 +ch3 330 340 0.0 0.0 +ch3 340 350 0.0 0.0 +ch3 350 360 0.0 0.0 +ch3 360 370 0.0 0.0 +ch3 370 380 0.0 0.0 +ch3 380 390 0.0 0.0 +ch3 390 400 0.0 0.0 diff -r a4ecef241a6d -r 0d2ba04b8261 test-data/test_compated.bw Binary file test-data/test_compated.bw has changed diff -r a4ecef241a6d -r 0d2ba04b8261 test-data/test_half.bw Binary file test-data/test_half.bw has changed