Mercurial > repos > proteore > proteore_filter_keywords_values

annotate README.rst @ 5:33ca9ba2495a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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author proteore
date Tue, 05 Mar 2019 07:37:10 -0500
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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.