Mercurial > repos > galaxyp > fastg2protlib
annotate application.py @ 0:6b226c5907a1 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
| author | galaxyp |
|---|---|
| date | Fri, 07 Aug 2020 06:17:31 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
|
0
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
1 import argparse |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
2 |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
3 import fastg2protlib.fastg2protlib as fg |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
4 |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
5 expasy_rules = [ |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
6 "arg-c", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
7 "asp-n", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
8 "bnps-skatole", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
9 "caspase 1", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
10 "caspase 2", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
11 "caspase 3", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
12 "caspase 4", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
13 "caspase 5", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
14 "caspase 6", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
15 "caspase 7", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
16 "caspase 8", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
17 "caspase 9", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
18 "caspase 10", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
19 "chymotrypsin high specificity", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
20 "chymotrypsin low specificity", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
21 "clostripain", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
22 "cnbr", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
23 "enterokinase", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
24 "factor xa", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
25 "formic acid", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
26 "glutamyl endopeptidase", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
27 "granzyme b", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
28 "hydroxylamine", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
29 "iodosobenzoic acid", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
30 "lysc", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
31 "ntcb", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
32 "pepsin ph1.3", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
33 "pepsin ph2.0", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
34 "proline endopeptidase", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
35 "proteinase k", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
36 "staphylococcal peptidase i", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
37 "thermolysin", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
38 "thrombin", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
39 "trypsin", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
40 "trypsin_exception", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
41 ] |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
42 |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
43 |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
44 if __name__ == "__main__": |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
45 parser = argparse.ArgumentParser(description="Run peptides for fastg") |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
46 parser.add_argument("fastg", help="Path to Spades formatted FASTG.") |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
47 parser.add_argument( |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
48 "-d", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
49 "--dbname", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
50 default="results.db", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
51 help="Name for the results database. Defaults to results.db", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
52 ) |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
53 parser.add_argument( |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
54 "-c", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
55 "--cleavage", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
56 default="trypsin", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
57 help="Cleavage rule from ExPASy cleavage rules. Defaults to trypsin.", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
58 ) |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
59 parser.add_argument( |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
60 "-p", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
61 "--min_protein_length", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
62 default=55, |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
63 type=int, |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
64 help="Minimum protein length in number of amino acids. Defaults to 55.", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
65 ) |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
66 parser.add_argument( |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
67 "-m", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
68 "--min_peptide_length", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
69 default=8, |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
70 type=int, |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
71 help="Minimum peptide length in amino acids. Defaults to eight.", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
72 ) |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
73 parser.add_argument( |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
74 "-l", "--plots", default=True, type=bool, help="Generate diagnostic plots.", |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
75 ) |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
76 |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
77 args = parser.parse_args() |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
78 |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
79 print(args) |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
80 |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
81 fg.peptides_for_fastg( |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
82 fastg_filename=args.fastg, |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
83 db_name=args.dbname, |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
84 cleavage=args.cleavage, |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
85 min_protein_length=(args.min_protein_length * 3), |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
86 min_peptide_length=args.min_peptide_length, |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
87 create_plots=args.plots, |
|
6b226c5907a1
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
galaxyp
parents:
diff
changeset
|
88 ) |