Mercurial > repos > proteore > filter_keywords_values

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Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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author proteore
date Wed, 07 Mar 2018 08:44:34 -0500
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1 Wrapper for Filter out keywords and/or numerical values tool 1 Wrapper for Filter by keywords or numerical values Tool
2 ============================================================ 2 =======================================================
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4 **Authors** 4 **Authors**
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6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 6 T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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7 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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9 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 10 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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11 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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13 ------------------------------------------------------------ 14 -------------------------------------------------------
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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 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 **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 **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**
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19 **Filter the file by keywords** 20 **Filter the file by keywords**
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21 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. 22 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 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175
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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 26 - If you choose to upload a file in a text format in which each line is a keyword, for example:
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29 TRYP_PIG 28 REV
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31 ALDOA_RABBIT 30 TRYP_PIG
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32 ALDOA_RABBIT
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33 **The line that contains these keywords will be eliminated from input file.** 34 **The line that contains these keywords will be eliminated from input file.**
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35 **Keywords search can be applied by performing either exact match or partial one by using the following option** 36 **Keywords search can be applied by performing either exact match or partial one by using the following option**
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37 - If you choose **Yes**, only the fields that contains exactly the same content will be removed. 38 - 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 - If you choose **No**, all the fields containing the keyword will be removed.
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41 For example: 42 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 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed.
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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 **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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47 **Filter the file by values** 48 **Filter the file by values**
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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 You can choose to use one or more options (e.g. to filter out peptides of low intensity value, by q-value, etc.).
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51 * For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option. 52 * For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option.
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55 The tool will produce 2 output files. 56 The tool will produce 2 output files.
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57 * A text file containing the resulting filtered input file. 58 * A text file containing the resulting filtered input file.
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59 * A text file containing the rows removed from the input file. 60 * A text file containing the rows removed from the input file.
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