Merge branch 'master' of github.com:BMCV/galaxy-image-analysis into bioformats2raw-0.7.0 #1
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Also updates bio.tools and biii xrefs.
* adds code of conduct Adds code of conduct from galaxyproject/tools-iuc repo. * adds matrix badge * adds DOI badge * changes matrix badge color * adds list of tools * adds contribution instructions * fixes link in README.md * updates CONTRIBUTING.md * updates README.md * fixes some issues * updates PR template * removes versions from tool list in README.md
adapts environment variables and annotations for SuperDSM
imaging 2d_simple_filter: changed input label to "Filter type"
The changes follow those made in 9c6cad866c707cdb7d93cb56a48718030cc2a6c1.
* changed default output to png for seg_contour * fixed output filter * bump version number * added expect_num_outputs="1" also fixed lint errors for the output name and label * decreased file size of png somehow, the github CI produces a smaller png file. opened the PNG in GIMP and saved it with compression 9 and without exif data. --------- Co-authored-by: Björn Grüning <[email protected]>
Skip lint on merge / minor other repo updates
trigger ci, deploy missing tools
trigger ci, deploy missing tools from BMCV#76
trigger ci, deploy missing tools from BMCV#76
temporarily skip xsd linting during deployment
* adds zenodo citation to segmetrics tool * removes zenodo reference, adds version macros
The SuperDSM wrapper accepts only even numbers for `seg_border`.
Segmentation is skipped if neither label map nor the report of the hyperparameters is requested.
add bioformats2raw
fixes `owner` of `bioformats2raw` tool
This correction is due to BMCV#96 (comment) and should be right judging by 34c2bc0.
fixes `remote_repository_url` in `bioformats2raw`
update multiple tools
Fixes bug in `overlay_images` tool which occured when 16bit images were used for input to produce segmentation overlays (instead of 8bit).
Looks like that 45655df was not wrong after all, but you have to use `--biocontainers` with `planemo test` in order to obtain the same results as the CI.
…ioformats2raw-0.7.0
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xref BMCV#99
FOR CONTRIBUTOR: