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It seems planemo is uploading unwanted files to the Tool Shed with individual tool uploads. In some cases it uploads multiple tools from a demultiplexed git repository into a single tool repository, while in other cases it uploads unwanted files from other tools.
The individual ImageJ2 tools are demultiplexed in here: https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2
Planemo uploaded each of these tools to the TTS, including every ImageJ2 tool in each individual repo:
Repository 'imagej2_adjust_threshold_binary' revision c05d862ac753 (repository tip)
Contents:
imagej2_adjust_threshold_binary.py
imagej2_adjust_threshold_binary.xml
imagej2_adjust_threshold_binary_jython_script.py
imagej2_analyze_particles_binary.py
imagej2_analyze_particles_binary_jython_script.py
imagej2_analyze_skeleton.py
imagej2_analyze_skeleton_jython_script.py
...
On the MTS, the meme tool repo contains the fimo tool's Python script:
Repository 'meme_meme' revision 487ce3fa1822 (repository tip)
Contents:
all_fasta.loc.sample
fimo_wrapper.py
meme.xml
test-data/
tool_data_table_conf.xml.sample
tool_dependencies.xml
There are other similar examples on both the TTS and MTS.
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