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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:33:28 +0000
parents 25529df60a81
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15:25529df60a81 16:06cca574e337
9 9
10 * https://github.com/OpenMS/OpenMS 10 * https://github.com/OpenMS/OpenMS
11 * https://www.openms.de/ 11 * https://www.openms.de/
12 12
13 The wrappers for these tools and most of their tests are automatically 13 The wrappers for these tools and most of their tests are automatically
14 generated using the `generate.sh` script. The generation of the tools is 14 generated using the `./aux/generate.sh` script. The generation of the tools is
15 based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter) 15 based on the CTDConverter (https://github.com/WorkflowConversion/CTDConverter)
16 which can be fine tuned via the `hardcoded_params.json` file. This file allows 16 which can be fine tuned via the `hardcoded_params.json` file. This file allows
17 to blacklist and hardcode parameters and to modify or set arbitrary 17 to blacklist and hardcode parameters and to modify or set arbitrary
18 CTD/XML attributes. 18 CTD/XML attributes.
19 19
127 More details can be found in the comments of the shell script. 127 More details can be found in the comments of the shell script.
128 128
129 Open problems 129 Open problems
130 ============= 130 =============
131 131
132 Some tools stall in CI testing using `--biocontainers` which is why the OpenMS
133 tools are currently listed in `.tt_biocontainer_skip`. This is
134
135 - AssayGeneratorMetabo and SiriusAdapter (both depend on sirius)
136 - OMSSAAdapter
137
138 Using `docker -t` seems to solve the problem (see
139 https://github.com/galaxyproject/galaxy/issues/10153).
140
141 Licence (MIT) 132 Licence (MIT)
142 ============= 133 =============
143 134
144 Permission is hereby granted, free of charge, to any person obtaining a copy 135 Permission is hereby granted, free of charge, to any person obtaining a copy
145 of this software and associated documentation files (the "Software"), to deal 136 of this software and associated documentation files (the "Software"), to deal