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annotate generate_workflow.py @ 9:1455d3e7f191 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
author galaxyp
date Fri, 16 Jan 2026 09:34:00 +0000
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9
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
galaxyp
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1 #!/usr/bin/env python3
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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2
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3 #
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4 # Generates a FragPipe Workflow file.
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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5 #
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6
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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7 import pathlib
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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8 import sys
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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9
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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10 default_workflow = sys.argv[1]
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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11 user_params_filename = sys.argv[2]
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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12 output_workflow_filename = sys.argv[3]
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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14 # Default workflow as packaged in the Galaxy $__tool_directory__
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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15 default_workflow_path = pathlib.Path(__file__).resolve().parent.joinpath(f'workflows/{default_workflow}.workflow')
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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17 # Collect comments separately from parameters
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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18 comments = []
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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20 # Dictionary with workflow parameters
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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21 wfdict = {}
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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23 # Initialize workflow dictionary with defaults
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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24 with open(default_workflow_path, 'r') as inf:
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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25 for line in inf:
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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26 if line.startswith('#'):
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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27 comments.append(line)
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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28 elif line.strip() != '':
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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29 kv = line.strip().split('=')
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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30 if len(kv) < 2:
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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31 kv.append('')
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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32 wfdict[kv[0]] = '='.join(kv[1:])
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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33
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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34 # Overwrite with user parameters from Galaxy
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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35 with open(user_params_filename, 'r') as inf:
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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36 for line in inf:
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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37 if line.strip() != '':
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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38 kv = line.strip().split('=')
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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39 if len(kv) < 2:
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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40 kv.append('')
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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41 wfdict[kv[0]] = '='.join(kv[1:])
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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42
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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43 # Output comments and parameter definitions to workflow file
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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44 with open(output_workflow_filename, 'w') as outf:
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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45 for comment in comments:
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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46 print(comment, file=outf)
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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47 for k in sorted(wfdict.keys()):
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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48 kv = f'{k}={wfdict[k]}'
1455d3e7f191 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 02d7c1a0439315c2868c0e66d74fd567e89cca02
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49 print(kv, file=outf)