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author | proteore |
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date | Wed, 19 Sep 2018 05:01:15 -0400 |
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1 Wrapper for Filter by keywords or numerical values Tool | |
2 ======================================================= | |
3 | |
4 **Authors** | |
5 | |
6 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR | |
7 | |
8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform | |
9 | |
10 This work has been partially funded through the French National Agency for Research (ANR) IFB project. | |
11 | |
12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. | |
13 | |
14 ------------------------------------------------------- | |
15 | |
16 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). | |
17 | |
18 **Filter by keyword(s)** | |
19 | |
20 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. | |
21 | |
22 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175 | |
23 | |
24 - If you choose to upload a file in a text format in which each line is a keyword, for example: | |
25 | |
26 REV | |
27 | |
28 TRYP_PIG | |
29 | |
30 ALDOA_RABBIT | |
31 | |
32 **The line that contains these keywords will be eliminated from input file.** | |
33 | |
34 **Keywords search can be applied by performing either exact match or partial one by using the following option** | |
35 | |
36 - If you choose **Yes**, only the fields that contains exactly the same content will be removed. | |
37 | |
38 - If you choose **No**, all the fields containing the keyword will be removed. | |
39 | |
40 For example: | |
41 | |
42 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. | |
43 | |
44 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. | |
45 | |
46 ------------------------------------------------------- | |
47 | |
48 **Filter by values** | |
49 | |
50 You can filter your data by a column of numerical values. | |
51 Enter the column to be use and select one operator in the list : | |
52 | |
53 - = | |
54 - != | |
55 - < | |
56 - <= | |
57 - > | |
58 - >= | |
59 | |
60 Then enter the value to filter and specify the column to apply that option. | |
61 If a row contains a value that correspond to your settings, it will be filtered. | |
62 | |
63 ------------------------------------------------------- | |
64 | |
65 **Filter by a range of values** | |
66 | |
67 You can also set a range of values to filter your file. | |
68 In opposition to value filter, rows with values inside of the defined range are kept. | |
69 | |
70 Rows with values outside of the defined range will be filtered. | |
71 | |
72 ------------------------------------------------------- | |
73 | |
74 **AND/OR operator** | |
75 | |
76 Since you can add as many filters as you want, you can choose how filters apply on your data. | |
77 | |
78 AND or OR operator option works on all filters : | |
79 | |
80 - OR : only one filter to be satisfied to remove one row | |
81 - AND : all filters must be satisfied to remove one row | |
82 | |
83 ------------------------------------------------------- | |
84 | |
85 **Sort the results files** | |
86 | |
87 You can sort the result file if you wish, it can help you to check results. | |
88 | |
89 In order to do so : enter the column to be used, all columns will be sorted according to the one filled in. | |
90 | |
91 Rows stay intact, just in different order like excel. | |
92 You can also choose ascending or descending order, by default descending order is set. | |
93 | |
94 ------------------------------------------------------- | |
95 | |
96 **Output** | |
97 | |
98 The tool will produce 2 output files. | |
99 | |
100 * A text file containing the resulting filtered input file. | |
101 | |
102 * A text file containing the rows removed from the input file. |