Mercurial > repos > goeckslab > scimap_mcmicro_to_anndata
changeset 5:b1ead1b7e0aa draft default tip
planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 78a4f1a616a9b7f7ca71cdf32e6a63a1daeec8bf
| author | goeckslab |
|---|---|
| date | Wed, 11 Jun 2025 22:18:38 +0000 |
| parents | 49c178651194 |
| children | |
| files | main_macros.xml mcmicro_to_anndata.py mcmicro_to_anndata.xml |
| diffstat | 3 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/main_macros.xml Tue Jul 30 18:20:49 2024 +0000 +++ b/main_macros.xml Wed Jun 11 22:18:38 2025 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.1.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> <token name="@PROFILE@">20.01</token> <xml name="scimap_requirements">
--- a/mcmicro_to_anndata.py Tue Jul 30 18:20:49 2024 +0000 +++ b/mcmicro_to_anndata.py Wed Jun 11 22:18:38 2025 +0000 @@ -20,13 +20,17 @@ with open(inputs, 'r') as param_handler: params = json.load(param_handler) - image_path = params['image_path'] + image_path = params['image_path']['source_path'] drop_markers = params['drop_markers'] if not drop_markers: drop_markers = None else: drop_markers = [x.strip() for x in drop_markers.split(',')] options = params['options'] + if not options.get('custom_imageid'): + element_identifier = params['image_path']['element_identifier'] + # Might be a list on unpatched versions of Galaxy, xref: https://github.com/galaxyproject/galaxy/pull/20438 + options['custom_imageid'] = element_identifier if isinstance(element_identifier, str) else element_identifier[0] for k, v in options.items(): if v == '': options[k] = None
--- a/mcmicro_to_anndata.xml Tue Jul 30 18:20:49 2024 +0000 +++ b/mcmicro_to_anndata.xml Wed Jun 11 22:18:38 2025 +0000 @@ -15,7 +15,7 @@ ]]> </command> <configfiles> - <inputs name="inputs" data_style="paths"/> + <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param argument="image_path" type="data" format="tabular,csv" multiple="false" label="Select the input image or images" />