Mercurial > repos > proteore > filter_keywords_values

annotate README.rst @ 0:6a45ccfc0e4c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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author proteore
date Sun, 26 Nov 2017 18:36:43 -0500
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1 Wrapper for Filter out keywords and/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, 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
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8
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9 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.
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13 ------------------------------------------------------------
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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).
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16
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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**
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18
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19 **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.
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22
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23 - 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
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29 TRYP_PIG
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31 ALDOA_RABBIT
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33 **The line that contains these keywords will be eliminated from input file.**
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34
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35 **Keywords search can be applied by performing either exact match or partial one by using the following option**
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36
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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.
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40
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41 For example:
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42
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43 **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.
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46
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47 **Filter the file by values**
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48
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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.).
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50
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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.
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52
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53 **Output**
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55 The tool will produce 2 output files.
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56
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57 * A text file containing the resulting filtered input file.
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58
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59 * A text file containing the rows removed from the input file.
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