Mercurial > repos > iuc > mzmine_batch

annotate set_path.py @ 1:90d60c9da21e draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
author iuc
date Fri, 10 Nov 2023 14:20:45 +0000
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90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
diff changeset
1 import argparse
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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2 import re
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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3 import sys
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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4 from xml.etree import ElementTree
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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5
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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6 parser = argparse.ArgumentParser(
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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7 prog="set_path.py", description="update paths in mzmine batch XML"
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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8 )
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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9 parser.add_argument("--input", help="input XML")
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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10 parser.add_argument("--output", help="output XML")
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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11 parser.add_argument("--localdb", required=False, help="Local CVS DB for Search")
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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12 args = parser.parse_args()
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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14 PATHSEP = re.compile(r"[/\\]")
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
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15 tree = ElementTree.parse(args.input)
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
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90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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17 for batchstep in tree.findall(".//batchstep"):
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
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18 method = batchstep.attrib.get("method")
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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19 for current_file in batchstep.findall(".//current_file"):
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
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20 if (
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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21 method
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
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22 == "io.github.mzmine.modules.dataprocessing.id_localcsvsearch.LocalCSVDatabaseSearchModule"
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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23 ):
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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24 if args.localdb:
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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25 current_file.text = args.localdb
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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26 else:
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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27 sys.exit("Batch file contains LocalCSVDatabaseSearchModule but no local DB CSV file given")
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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28 else:
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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29 current_file.text = f"./output/{PATHSEP.split(current_file.text)[-1]}"
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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30
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
iuc
parents:
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31 tree.write(args.output)