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annotate operation_filter.py @ 6:4d584cf5ced5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
author devteam
date Mon, 13 Jun 2022 16:26:51 +0000
parents 37652c34b3bf
children
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1 # runs after the job (and after the default post-filter)
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2 from galaxy.tools.parameters import DataToolParameter
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4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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5 def validate_input(trans, error_map, param_values, page_param_map):
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6 dbkeys = set()
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7 data_param_names = set()
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8 data_params = 0
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9 for name, param in page_param_map.items():
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4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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10 if isinstance(param, DataToolParameter):
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11 # for each dataset parameter
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12 if param_values.get(name, None) is not None:
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4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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13 dbkeys.add(param_values[name].dbkey)
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14 data_params += 1
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15 # check meta data
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16 try:
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17 param = param_values[name]
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4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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18 if isinstance(param.datatype, trans.app.datatypes_registry.get_datatype_by_extension('gff').__class__):
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19 # TODO: currently cannot validate GFF inputs b/c they are not derived from interval.
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20 pass
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21 else: # Validate interval datatype.
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4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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22 int(param.metadata.startCol)
4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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23 int(param.metadata.endCol)
4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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24 int(param.metadata.chromCol)
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25 if param.metadata.strandCol is not None:
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4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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26 int(param.metadata.strandCol)
4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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27 except Exception:
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28 error_msg = "The attributes of this dataset are not properly set. " + \
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29 "Click the pencil icon in the history item to set the chrom, start, end and strand columns."
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30 error_map[name] = error_msg
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4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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31 data_param_names.add(name)
4d584cf5ced5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/basecoverage commit 200bd4645dd768eb6ee1aab7d181b76d34d13d4c
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32 if len(dbkeys) > 1:
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33 for name in data_param_names:
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34 error_map[name] = "All datasets must belong to same genomic build, " \
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35 "this dataset is linked to build '%s'" % param_values[name].dbkey
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36 if data_params != len(data_param_names):
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37 for name in data_param_names:
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38 error_map[name] = "A dataset of the appropriate type is required"
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39
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41 def exec_after_merge(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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42 # strip strand column if clusters were merged
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43 for data in out_data.values():
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44 if param_dict['returntype'] is True:
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45 data.metadata.chromCol = 1
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46 data.metadata.startCol = 2
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47 data.metadata.endCol = 3
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48 # merge always clobbers strand
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49 data.metadata.strandCol = None
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52 def exec_after_cluster(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None):
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53 # strip strand column if clusters were merged
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54 if param_dict["returntype"] == '1':
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55 for data in out_data.values():
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56 data.metadata.strandCol = None