Mercurial > repos > galaxyp > maxquant_mqpar
annotate mqwrapper.py @ 2:b95d333b4a3f draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 74b5aa29e49deaaebe19ce2355a70d4f570f4951"
| author | galaxyp |
|---|---|
| date | Thu, 15 Aug 2019 08:08:23 -0400 |
| parents | 081720f095a9 |
| children |
| rev | line source |
|---|---|
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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1 """ |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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2 Run MaxQuant on a modified mqpar.xml. |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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3 Use maxquant conda package. |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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4 TODO: add support for parameter groups |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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5 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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6 Authors: Damian Glaetzer <d.glaetzer@mailbox.org> |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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7 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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8 based on the maxquant galaxy tool by John Chilton: |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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9 https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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10 """ |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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11 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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12 import argparse |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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13 import os |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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14 import shutil |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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15 import subprocess |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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16 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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17 import mqparam |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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18 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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19 # build parser |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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20 parser = argparse.ArgumentParser() |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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21 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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22 # input, special outputs and others |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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23 other_args = ('raw_files', 'mzxml_files', 'fasta_files', |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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24 'description_parse_rule', 'identifier_parse_rule', |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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25 'mqpar_in', 'output_all', |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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26 'mqpar_out', 'infile_names', 'mzTab', |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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27 'version', 'substitution_rx') |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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28 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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29 # txt result files |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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30 txt_output = ('evidence', 'msms', 'parameters', |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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31 'peptides', 'proteinGroups', 'allPeptides', |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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32 'libraryMatch', 'matchedFeatures', |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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33 'modificationSpecificPeptides', 'ms3Scans', |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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34 'msmsScans', 'mzRange', 'peptideSection', |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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35 'summary') |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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36 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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37 global_simple_args = ('num_threads',) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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38 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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39 arguments = ['--' + el for el in (txt_output |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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40 + other_args |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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41 + global_simple_args)] |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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42 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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43 for arg in arguments: |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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44 parser.add_argument(arg) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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45 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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46 args = vars(parser.parse_args()) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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47 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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48 # link infile datasets to names with correct extension |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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49 # for maxquant to accept them |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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50 files = (args['raw_files'] if args['raw_files'] |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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51 else args['mzxml_files']).split(',') |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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52 ftype = ".thermo.raw" if args['raw_files'] else ".mzXML" |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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53 filenames = args['infile_names'].split(',') |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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54 fnames_with_ext = [(a if a.endswith(ftype) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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55 else os.path.splitext(a)[0] + ftype) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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56 for a in filenames] |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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57 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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58 for f, l in zip(files, fnames_with_ext): |
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1
081720f095a9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 2131f017e9303599ed672797ffd6e9b00ab1245d
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59 os.symlink(f, l) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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60 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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61 # build mqpar.xml |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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62 mqpar_temp = os.path.join(os.getcwd(), 'mqpar.xml') |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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63 mqpar_out = args['mqpar_out'] if args['mqpar_out'] != 'None' else mqpar_temp |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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64 mqpar_in = args['mqpar_in'] |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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65 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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66 exp_design = None |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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67 m = mqparam.MQParam(mqpar_out, mqpar_in, exp_design, |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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68 substitution_rx=args['substitution_rx']) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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69 if m.version != args['version']: |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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70 raise Exception('mqpar version is ' + m.version + |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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71 '. Tool uses version {}.'.format(args['version'])) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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72 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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73 # modify parameters, interactive mode if no mqpar_in was specified |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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74 m.add_infiles([os.path.join(os.getcwd(), name) for name in fnames_with_ext], False) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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75 m.add_fasta_files(args['fasta_files'].split(','), |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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76 identifier=args['identifier_parse_rule'], |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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77 description=args['description_parse_rule']) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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78 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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79 m.write() |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
parents:
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80 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
galaxyp
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81 # build and run MaxQuant command |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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82 cmd = ['maxquant', mqpar_out] |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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83 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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84 subprocess.run(cmd, check=True, cwd='./') |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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85 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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86 # copy results to galaxy database |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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87 for el in txt_output: |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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88 destination = args[el] |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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89 source = os.path.join(os.getcwd(), "combined", "txt", "{}.txt".format(el)) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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90 if destination != 'None' and os.path.isfile(source): |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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91 shutil.copy(source, destination) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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92 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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93 if args['mzTab'] != 'None': |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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94 source = os.path.join(os.getcwd(), "combined", "txt", "mzTab.mzTab") |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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95 if os.path.isfile(source): |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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96 shutil.copy(source, args['mzTab']) |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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97 |
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a52165553917
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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98 if args['output_all'] != 'None': |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit ab4e4f1817080cbe8a031a82cb180610ff140847
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99 subprocess.run(('tar', '-zcf', args['output_all'], './combined/txt/')) |