Mercurial > repos > proteore > proteore_filter_keywords_values
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author | proteore |
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date | Wed, 19 Sep 2018 05:01:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Sep 19 05:01:15 2018 -0400 @@ -0,0 +1,102 @@ +Wrapper for Filter by keywords or numerical values Tool +======================================================= + +**Authors** + +T.P. Lien Nguyen, David Christiany, 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). + +**Filter by keyword(s)** + +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 by values** + +You can filter your data by a column of numerical values. +Enter the column to be use and select one operator in the list : + +- = +- != +- < +- <= +- > +- >= + +Then enter the value to filter and specify the column to apply that option. +If a row contains a value that correspond to your settings, it will be filtered. + +------------------------------------------------------- + +**Filter by a range of values** + +You can also set a range of values to filter your file. +In opposition to value filter, rows with values inside of the defined range are kept. + +Rows with values outside of the defined range will be filtered. + +------------------------------------------------------- + +**AND/OR operator** + +Since you can add as many filters as you want, you can choose how filters apply on your data. + +AND or OR operator option works on all filters : + +- OR : only one filter to be satisfied to remove one row +- AND : all filters must be satisfied to remove one row + +------------------------------------------------------- + +**Sort the results files** + +You can sort the result file if you wish, it can help you to check results. + +In order to do so : enter the column to be used, all columns will be sorted according to the one filled in. + +Rows stay intact, just in different order like excel. +You can also choose ascending or descending order, by default descending order is set. + +------------------------------------------------------- + +**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. \ No newline at end of file