Mercurial > repos > proteore > proteore_filter_keywords_values
annotate README.rst @ 7:5621406a4d2f draft
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author | proteore |
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date | Fri, 28 Jun 2019 05:09:20 -0400 |
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1 Wrapper for Filter by keywords or numerical values Tool |
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2 ======================================================= |
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3 |
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4 **Authors** |
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5 |
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6 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
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7 |
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8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform |
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9 |
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10 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
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11 |
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12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. |
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13 |
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14 ------------------------------------------------------- |
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15 |
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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). |
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17 |
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18 **Filter by keyword(s)** |
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19 |
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20 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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21 |
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22 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175 |
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23 |
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24 - If you choose to upload a file in a text format in which each line is a keyword, for example: |
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25 |
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26 REV |
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27 |
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28 TRYP_PIG |
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29 |
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30 ALDOA_RABBIT |
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31 |
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32 **The line that contains these keywords will be eliminated from input file.** |
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33 |
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34 **Keywords search can be applied by performing either exact match or partial one by using the following option** |
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35 |
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36 - If you choose **Yes**, only the fields that contains exactly the same content will be removed. |
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37 |
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38 - If you choose **No**, all the fields containing the keyword will be removed. |
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39 |
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40 For example: |
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41 |
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42 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. |
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43 |
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44 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. |
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45 |
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46 ------------------------------------------------------- |
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47 |
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48 **Filter by values** |
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49 |
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50 You can filter your data by a column of numerical values. |
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51 Enter the column to be use and select one operator in the list : |
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52 |
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53 - = |
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54 - != |
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55 - < |
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56 - <= |
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57 - > |
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58 - >= |
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59 |
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60 Then enter the value to filter and specify the column to apply that option. |
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61 If a row contains a value that correspond to your settings, it will be filtered. |
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62 |
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63 ------------------------------------------------------- |
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64 |
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65 **Filter by a range of values** |
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66 |
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67 You can also set a range of values to filter your file. |
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68 In opposition to value filter, rows with values inside of the defined range are kept. |
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69 |
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70 Rows with values outside of the defined range will be filtered. |
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71 |
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72 ------------------------------------------------------- |
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73 |
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74 **AND/OR operator** |
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75 |
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76 Since you can add as many filters as you want, you can choose how filters apply on your data. |
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77 |
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78 AND or OR operator option works on all filters : |
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79 |
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80 - OR : only one filter to be satisfied to remove one row |
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81 - AND : all filters must be satisfied to remove one row |
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82 |
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83 ------------------------------------------------------- |
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84 |
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85 **Sort the results files** |
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86 |
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87 You can sort the result file if you wish, it can help you to check results. |
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88 |
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89 In order to do so : enter the column to be used, all columns will be sorted according to the one filled in. |
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90 |
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91 Rows stay intact, just in different order like excel. |
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92 You can also choose ascending or descending order, by default descending order is set. |
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93 |
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94 ------------------------------------------------------- |
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95 |
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96 **Output** |
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97 |
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98 The tool will produce 2 output files. |
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99 |
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100 * A text file containing the resulting filtered input file. |
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101 |
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102 * A text file containing the rows removed from the input file. |