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1 [TOC]
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3 # 1. cfg_get_glycan_from_cells.py
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4
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5 Retrieve glycan profiling data from the CFG.
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6
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7 With focus on retrieving the annotated mass spec data (.msa files)
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8
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9 ## Works with Galaxy?
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10 Yes. see [getcfgcells.xml](getcfgcells.xml)
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11
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12 ## Command line usage
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13 ```
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14 ../../virtualpy/bin/activate
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15 python cfg_get_glycan_from_cells.py
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16 ```
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17
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18 This will use the default settings and by default pull all data from the CFG. This may take some time.
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19 The CFG may be unimpressed, if you do this too often.
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20
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21 To specify which data you would like to retrieve :
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22 ```
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23 ../../virtualpy/bin/activate
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24 cfg_get_glycan_from_cells.py -s "$species" -p "$investigator" -g "$glycantype" -c "$celltype" -o "$html_file" --filepath "msa_output"
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25 ```
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26
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27 ## Help
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28 ```
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29 ../../virtualpy/bin/activate
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30 python cfg_get_glycan_from_cells.py -h
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31 ```
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32
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33 ## Unit Testing?
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34 Not yet! Although some testing ha been done using the htmlfortesting.html and short-htmlfortesting.html. This code has also been used within Galaxy to retrieve data.
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35 So it _should work just fine..._
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36
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37 In principle:
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38
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39 ```
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40 ../../virtualpy/bin/activate
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41 python test_cfg_get_glycan_from_cells.py
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42 ```
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