Mercurial > repos > proteore > filter_keywords_values
annotate README.rst @ 1:d29e469b6b20 draft
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author | proteore |
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date | Fri, 16 Feb 2018 03:27:43 -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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10 |
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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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12 |
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13 ------------------------------------------------------------ |
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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). |
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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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20 |
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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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24 |
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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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26 |
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27 REV |
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28 |
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29 TRYP_PIG |
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30 |
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31 ALDOA_RABBIT |
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32 |
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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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38 |
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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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44 |
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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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54 |
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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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60 |
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62 |