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… and image format
…d update documentation
…ssage construction
* Add dotPrep tool * Change repository name to Lowercase * Fix linting and flake8 errors * Fix flake8 for script * Perhaps this makes the linter happy * One more try :) * Readjust test parameters
… 1.3.46 (bgruening#1710) Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Co-authored-by: Leonid Kostrykin <void@evoid.de>
* add py3dtiles * Update 3D Trees Py3DTiles Converter tool name and Docker container reference * added error handling * updated the xml wirth macros * create folder with permissions * Update output directory references in py3dtiles.xml to use the current directory instead of tiles_output * changing output dir * added lastest docker image * remove the compare test data * added test for collection * Update tools/3dtrees_py3dtiles/py3dtiles.xml --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
* Update til_mer.xml: increment version suffix to 1, adjust output file references, and ensure consistent thread parameter usage in commands * move the threads out of conditional
* resolve tool version issue * increase galaxy tool shed version * update xml * update overview tool for migration * remove indent * env vars defined in docker
Co-authored-by: Leonid Kostrykin <void@evoid.de>
Co-authored-by: Leonid Kostrykin <void@evoid.de>
Co-authored-by: Leonid Kostrykin <void@evoid.de>
…channels fix: cellpose headless tool
* bump version * update cox function * add user graph option * fix flake8 lint * fix cheetah * add coexpression method * add cox penalizer * restrict plot function * black lint * fix filters * fix test 6 * correct filter for plots * restrict safetensors to models that generate the file * add test for svm which does not create embedding or model * comment out test 20 for user graph * fix lint * update filter * fix flake 8 lint * clean up plot conditional * filter checks if variables exists first * fix cheetah * update filter * correct model filter * tests should pass * add safetensors filter in command * update if logic for safetensor * update if logic * correct if statement * comment out user_graph * disable progress bar --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
* add cellpose sam * add cellpose as requirement * udpates to cp4 * update test image size * shed linting error fix * updates * fixes * fixes * fixes and try again * fixes * fix pillow error * first round modifications,pending second round(validator+3d test case + others) * works temporarily, still pending other changes * Update tools/cellpose_v4/cellpose.xml Co-authored-by: Leonid Kostrykin <void@evoid.de> * add 3d test * fix test 4 * fix test 4 * linting error fix * Employ `image_diff` * fix indentation, removing epsw --------- Co-authored-by: Yi Sun <yi.sun@embl.de> Co-authored-by: Björn Grüning <bjoern@gruenings.eu> Co-authored-by: Leonid Kostrykin <void@evoid.de>
* Added m4a as input and output options for ffmpeg * Updated the test files and xml file to pass the planemo tests locally. * Improved tests and tests pass with biocontainer as well now. * Updated the tests to use asserts instead of sim_size * Removed unnecessary files to save space. --------- Co-authored-by: Armin Dadras <armindadras@fedora.fritz.box>
* Add kMetaShot and DM * add error test case * Apply suggestions from code review --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
* add Psortb * Update tools/psortb/psortb.xml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update tools/psortb/.shed.yml Co-authored-by: Björn Grüning <bjoern@gruenings.eu> * Update remote repository URL for psortb tool * Update remote repository URL to use 'master' branch --------- Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
…ing over the tool (bgruening#1740) * Add BAM collection input type * Remove bam collection input type in favour of modifying the existing bam/sam inputs Allow bam/sam input to accept multiple datasets for a single job instead of mapping them over the tool. * Bump galaxy version suffix * Add test for using multiple bam files Fixed crash when multiple datasets have the same name by adding a suffix when neccessary. * Add Bowtie2 warning message to BAM help section. This is a bug in Bowtie2 that vRhyme circumvents when it calls Bowtie2 internally, but cannot solve when the BAm files were already created. * Fix typo in test condition
* Fix bug in splitting fasta by chunks * Fix lint error
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