Dfpl#102
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* iphop: initial commit * DM fixes * disable tests * fix sample loc file * change URL * Apply suggestions from code review
* add new tools (omero get and omero filter) and updated the ci/pr pipeline to add metadat to the dummy set) * use conditionals to more explicitely indicate the id required. * fix annotation part * convert omero_get to omero_get_id * add get_value * add single quotes * Fix bad copy paste * add tests * remove unused f * remove unused function * fix function name * fix spaces * Updated all the scripts and xml files according to previous review * correct indentation of omero_filter and omero_get_id * Update omero_filter.py Fixed the error handling using sys * fixed code and xml from omero_filter for correct linting * correct image name * fixed indentation * fix the regex of omero_get_value and updated the sheed * fixed the regex to handle single number plus comma separated numbers * Fix testing in output and omero_get_value.xml * Correct the cheetah sintax in omero_get_value.xml * Correct the test in omero_get_value.xml - tsv output has 2 rows considering the header * Last corrections to the omero_get_value script to harmonize it with the other code style (writing tsv in write mode and error handling) * add macros * omero import do not expose password * add requirement macros * add host port token * bump * add macros file * fix macro expansion --------- Co-authored-by: Lucille Delisle <[email protected]> Co-authored-by: Matthias Bernt <[email protected]>
* add new tools (omero get and omero filter) and updated the ci/pr pipeline to add metadat to the dummy set) * use conditionals to more explicitely indicate the id required. * fix annotation part * convert omero_get to omero_get_id * add get_value * add single quotes * Fix bad copy paste * add tests * remove unused f * remove unused function * fix function name * fix spaces * Updated all the scripts and xml files according to previous review * correct indentation of omero_filter and omero_get_id * Update omero_filter.py Fixed the error handling using sys * fixed code and xml from omero_filter for correct linting * correct image name * fixed indentation * fix the regex of omero_get_value and updated the sheed * fixed the regex to handle single number plus comma separated numbers * Fix testing in output and omero_get_value.xml * Correct the cheetah sintax in omero_get_value.xml * Correct the test in omero_get_value.xml - tsv output has 2 rows considering the header * Last corrections to the omero_get_value script to harmonize it with the other code style (writing tsv in write mode and error handling) * add macros * omero import do not expose password * add requirement macros * add host port token * bump * add macros file * fix macro expansion * Added security disclaimers to the OMERO suite tools * Added macro for security disclaimer --------- Co-authored-by: Lucille Delisle <[email protected]> Co-authored-by: Matthias Bernt <[email protected]>
* add new tools (omero get and omero filter) and updated the ci/pr pipeline to add metadat to the dummy set) * use conditionals to more explicitely indicate the id required. * fix annotation part * convert omero_get to omero_get_id * add get_value * add single quotes * Fix bad copy paste * add tests * remove unused f * remove unused function * fix function name * fix spaces * Updated all the scripts and xml files according to previous review * correct indentation of omero_filter and omero_get_id * Update omero_filter.py Fixed the error handling using sys * fixed code and xml from omero_filter for correct linting * correct image name * fixed indentation * fix the regex of omero_get_value and updated the sheed * fixed the regex to handle single number plus comma separated numbers * Fix testing in output and omero_get_value.xml * Correct the cheetah sintax in omero_get_value.xml * Correct the test in omero_get_value.xml - tsv output has 2 rows considering the header * Last corrections to the omero_get_value script to harmonize it with the other code style (writing tsv in write mode and error handling) * add macros * omero import do not expose password * add requirement macros * add host port token * bump * add macros file * fix macro expansion * Added security disclaimers to the OMERO suite tools * Added macro for security disclaimer * Updated the tox tools - Now compounds name in the graph and in the excel output * add some validators and fix the plot output name * Fix the regex * fix the test to input according to regex<3 <2 * fix the regex * fix the regex, part2 * fix the regex, part 3 --------- Co-authored-by: Lucille Delisle <[email protected]> Co-authored-by: Matthias Bernt <[email protected]>
write to correct table
* phabox initial commit * review comments and add docs * add doc * add data manager
* DMs download data to extra_file_path * fix zenodo link * add lint skip for virsorter * fix plural * implement test mode for virsorter
* updated the shed.yml * add new tool for sheet extraction from xlx/xlsx file * Added the missing shed * Corrected some style problems with python code and the shed * updated both urls * Update xlsx2tsv.py - Changed the print output and deleted output_file variable * Update tools/wrangling/.shed.yml Co-authored-by: M Bernt <[email protected]> * changed folder name * correct the .sheed * Update tools/xls2tsv/.shed.yml --------- Co-authored-by: M Bernt <[email protected]>
* New tool for converting dataset to plate. CI/PR updated * Change Dataset 1 as target * Update omero_dataset_to_plate.xml * Delete .github/dummy_hcs_dataset directory * Update ci.yaml * Update pr.yaml * Update omero_dataset_to_plate.py * Update omero_dataset_to_plate.xml * Update omero_dataset_to_plate.py * updated the python script, more clear log file, add a dummy hcs dataset for upload in OMERO * correct the out file and the python script for writing * further correction of the log file * further correction of the test * Correction for the test output (xml + log file) * Further testing fixing * Further testing fixing - Worng ID * Correction of the log output file * Update tools/omero/omero_dataset_to_plate.xml Co-authored-by: M Bernt <[email protected]> * Added two additional inputs to the python file, mapping file plus dataset deletion option. Additionally, changed the style of the python code * PEP8 and log output file corrections * Further correction of the python code, changed append to write * Correct the log output file according to the new python script * Corrected the xml file * Corrected the python file * Added to the the metadata import script the OMERO objects Plate and Well * Add a min value id to all tools having an id as input * Update tools/omero/omero_dataset_to_plate.py Co-authored-by: M Bernt <[email protected]> * Update tools/omero/omero_metadata_import.xml Co-authored-by: M Bernt <[email protected]> * Update omero_dataset_to_plate.py * Update omero_dataset_to_plate.xml * correct the xml (data type missing) * string -> text as data type in the xml * Update omero_dataset_to_plate.xml * Update omero_dataset_to_plate.xml * Update omero_filter.xml * Update omero_filter.xml * test correction --------- Co-authored-by: M Bernt <[email protected]>
* Updates and fixes of the DR tool * Update dose_response.xml * Update tools/tox_tools/dose_responses/dose_response.xml Co-authored-by: M Bernt <[email protected]> * Correct the indentation of the R script * Correct the indentation of the R script * Correct the indentation of the R script using styler * Update tools/tox_tools/dose_responses/dose_response.xml * Update tools/tox_tools/dose_responses/dose_response.xml * Correct the image file dimension and add an LL4 model * New image output1 --------- Co-authored-by: M Bernt <[email protected]>
* wrapper for dfpl train
* remove `display` attribute from all selects
* remove unnecessary config file tag
* remove unnecessary true-/falsevalues, add citations, add min/max to numerical parameters
* add help text
* write zip directly to $output_model_weights
* tool version token for the tool version and the version requirement
* re-structured autoencoder parameters
* comment-out section "Weights & Biases"
* flatten folder structure
* output h5 files
* add min=5 for autoencoder epochs
* wrapper for dfpl predict
* .shed.yml file
* file ending .h5 instead of .hdf5
* update to 2.1 and add output assertions
* add sections and conditionals to tests
* link models instead of copying
* add validator for mandatory text parameter
* use mode wiespread command formatting
* introduce macros
* remove trailing dots
* add description
* bump dfpl version to 2.1
* fix linting: tool IDs with underscore instead of hyphen
* fix linting: use select parameter for conditional instead boolean
* fix linting: add output tests
* fix linting: address python flake8 complaints
* fix little {on_string} bug
* dfpl_predict: user-friendlier UI structure
* fetch test weights from URL
* fix linter errors
* fix linter errors v2
* fallback urls for absent test files
* check stdout instead of stderr for "Prediction successful"
* add organization description
* check stdout instead of stderr for success
---------
Co-authored-by: Matthias Bernt <[email protected]>
* add categories for dfpl (cherry picked from commit 5284b16) * Fix capitalization * add todo --------- Co-authored-by: M Bernt <[email protected]>
* fix omero dataset to plate * fixes it tests
* simple wrapper around SaQC for uploading config files * file sizes <1MB * add help text * add citation * correct repo URL Co-authored-by: M Bernt <[email protected]> * Remove stdout exit code specification Co-authored-by: M Bernt <[email protected]> * detect_errors="exit_code" Co-authored-by: M Bernt <[email protected]> * inline tests from macros.xml * remove unnecessary output label Co-authored-by: M Bernt <[email protected]> * add organization description * fix small xml bug * Minor reformulations --------- Co-authored-by: M Bernt <[email protected]>
* Fix the replicate column in the drc tool, removed the fixed column header, improved the help section * Update tools/tox_tools/dose_responses/dose_response.xml * Running the test in biocontainers * Correct the replicate legend label * Correct the replicate aesthetic in the plot --------- Co-authored-by: M Bernt <[email protected]>
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First version of the dfpl predictgnn wrap