# HG changeset patch # User proteore # Date 1520430274 18000 # Node ID 593b8a1b2a7bfc69bab7c14266fd4d3a278e6f42 # Parent 330d6c7b1916fe1f7c1b6adc0eee74bbddf97baf planemo upload commit f338a1cf9a782938c228f9bd0ea19ef22eec35d8-dirty diff -r 330d6c7b1916 -r 593b8a1b2a7b README.rst --- a/README.rst Thu Mar 01 08:15:55 2018 -0500 +++ b/README.rst Wed Mar 07 08:44:34 2018 -0500 @@ -1,16 +1,17 @@ -Wrapper for Filter out keywords and/or numerical values tool -============================================================ +Wrapper for Filter by keywords 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). @@ -20,30 +21,30 @@ 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: +- 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 - +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. - + +**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.). @@ -56,7 +57,4 @@ * A text file containing the resulting filtered input file. -* A text file containing the rows removed from the input file. - - - +* A text file containing the rows removed from the input file. \ No newline at end of file diff -r 330d6c7b1916 -r 593b8a1b2a7b filter_kw_val.xml --- a/filter_kw_val.xml Thu Mar 01 08:15:55 2018 -0500 +++ b/filter_kw_val.xml Wed Mar 07 08:44:34 2018 -0500 @@ -1,4 +1,4 @@ - + Filter a file by keywords or numerical values