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I would like to create a workflow to get several mbtile files by giving some informations like bboxes (wgs coordinates) or zoomlevels into it. The data should delivered from an tms source (mapproxy) for every given boundingbox/zoomlevel info. Does anyone know a software which is able for it? I have already checked gdal, tilemill, Globalmapper but nothing can export mbtiles out of an tms source.

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mapproxy-util export can create MBTiles from your existing caches. For example:

mapproxy-util export --grid GLOBAL_MERCATOR -f mapproxy.yaml \
    --source my_tile_cache --dest export.mbtiles --type mbtile \
    --levels 1..10 --fetch-missing-tiles --coverage 0,40,20,60 --srs epsg:4326

See: http://mapproxy.org/docs/nightly/mapproxy_util.html#export

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