Mercurial > repos > proteore > filter_keywords_values
diff README.rst @ 0:6a45ccfc0e4c draft
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author | proteore |
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date | Sun, 26 Nov 2017 18:36:43 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Sun Nov 26 18:36:43 2017 -0500 @@ -0,0 +1,62 @@ +Wrapper for Filter out keywords and/or numerical values tool +============================================================ + +**Authors** + +T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + +------------------------------------------------------------ + +This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). + +**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** + +**Filter the file by keywords** + +Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. + +- If you choose to fill in the field, the keywords should be separated by ":", for example: A8K2U0:Q5TA79:O43175 + +- If you choose to upload a file in a text format in which each line is a keyword, for example: + + REV + + TRYP_PIG + + ALDOA_RABBIT + +**The line that contains these keywords will be eliminated from input file.** + +**Keywords search can be applied by performing either exact match or partial one by using the following option** + +- If you choose **Yes**, only the fields that contains exactly the same content will be removed. + +- If you choose **No**, all the fields containing the keyword will be removed. + +For example: + +**Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. + +**No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. + +**Filter the file by values** + +You can choose to use one or more options (e.g. to filter out peptides of low intensity value, by q-value, etc.). + +* For each option, you can choose between "=", ">", ">=", "<" and "<=", then enter the value to filter and specify the column to apply that option. + +**Output** + +The tool will produce 2 output files. + +* A text file containing the resulting filtered input file. + +* A text file containing the rows removed from the input file. + + +