[WIP] ProteoRE 'filter kw and values' tool - Version 2021.06.01

tools/proteore_filter_keywords_values/.shed.yml

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+categories: [Proteomics]
+description: ProteoRE - Filter a file by keywords or values
+long_description: Filter a file by keywords or values
+name: proteore_filter_keywords_values
+owner: proteore
+include:
+  - README.rst
+  - filter_kw_val.py
+  - filter_kw_val.xml
+  - test-data/Lacombe_et_al_2017_OK.txt
+  - test-data/output.tsv
+  - test-data/discarded_lines.tsv

tools/proteore_filter_keywords_values/README.rst

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+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.