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author | proteore |
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date | Sun, 26 Nov 2017 18:36:43 -0500 |
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1 Wrapper for Filter out keywords and/or numerical values tool | |
2 ============================================================ | |
3 | |
4 **Authors** | |
5 | |
6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR | |
7 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform | |
8 | |
9 This work has been partially funded through the French National Agency for Research (ANR) IFB project. | |
10 | |
11 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. | |
12 | |
13 ------------------------------------------------------------ | |
14 | |
15 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). | |
16 | |
17 **For each row, if there are more than one protein IDs/protein names/gene names, only the first one will be considered in the output** | |
18 | |
19 **Filter the file by keywords** | |
20 | |
21 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. | |
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23 - If you choose to fill in the field, the keywords should be separated by ":", for example: A8K2U0:Q5TA79:O43175 | |
24 | |
25 - If you choose to upload a file in a text format in which each line is a keyword, for example: | |
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27 REV | |
28 | |
29 TRYP_PIG | |
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31 ALDOA_RABBIT | |
32 | |
33 **The line that contains these keywords will be eliminated from input file.** | |
34 | |
35 **Keywords search can be applied by performing either exact match or partial one by using the following option** | |
36 | |
37 - If you choose **Yes**, only the fields that contains exactly the same content will be removed. | |
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39 - If you choose **No**, all the fields containing the keyword will be removed. | |
40 | |
41 For example: | |
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43 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. | |
44 | |
45 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. | |
46 | |
47 **Filter the file by values** | |
48 | |
49 You can choose to use one or more options (e.g. to filter out peptides of low intensity value, by q-value, etc.). | |
50 | |
51 * For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option. | |
52 | |
53 **Output** | |
54 | |
55 The tool will produce 2 output files. | |
56 | |
57 * A text file containing the resulting filtered input file. | |
58 | |
59 * A text file containing the rows removed from the input file. | |
60 | |
61 | |
62 |