Mercurial > repos > proteore > proteore_filter_keywords_values
annotate README.rst @ 2:52a7afd01c6d draft
planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
author | proteore |
---|---|
date | Tue, 18 Dec 2018 09:25:11 -0500 |
parents | a55e8b137c6b |
children |
rev | line source |
---|---|
0
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
1 Wrapper for Filter by keywords or numerical values Tool |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
2 ======================================================= |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
3 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
4 **Authors** |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
5 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
6 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
7 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
8 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
9 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
10 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
11 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
12 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
13 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
14 ------------------------------------------------------- |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
15 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
16 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
17 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
18 **Filter by keyword(s)** |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
19 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
20 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
21 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
22 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
23 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
24 - If you choose to upload a file in a text format in which each line is a keyword, for example: |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
25 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
26 REV |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
27 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
28 TRYP_PIG |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
29 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
30 ALDOA_RABBIT |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
31 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
32 **The line that contains these keywords will be eliminated from input file.** |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
33 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
34 **Keywords search can be applied by performing either exact match or partial one by using the following option** |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
35 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
36 - If you choose **Yes**, only the fields that contains exactly the same content will be removed. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
37 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
38 - If you choose **No**, all the fields containing the keyword will be removed. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
39 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
40 For example: |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
41 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
42 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
43 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
44 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
45 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
46 ------------------------------------------------------- |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
47 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
48 **Filter by values** |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
49 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
50 You can filter your data by a column of numerical values. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
51 Enter the column to be use and select one operator in the list : |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
52 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
53 - = |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
54 - != |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
55 - < |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
56 - <= |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
57 - > |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
58 - >= |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
59 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
60 Then enter the value to filter and specify the column to apply that option. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
61 If a row contains a value that correspond to your settings, it will be filtered. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
62 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
63 ------------------------------------------------------- |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
64 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
65 **Filter by a range of values** |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
66 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
67 You can also set a range of values to filter your file. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
68 In opposition to value filter, rows with values inside of the defined range are kept. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
69 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
70 Rows with values outside of the defined range will be filtered. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
71 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
72 ------------------------------------------------------- |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
73 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
74 **AND/OR operator** |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
75 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
76 Since you can add as many filters as you want, you can choose how filters apply on your data. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
77 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
78 AND or OR operator option works on all filters : |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
79 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
80 - OR : only one filter to be satisfied to remove one row |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
81 - AND : all filters must be satisfied to remove one row |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
82 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
83 ------------------------------------------------------- |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
84 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
85 **Sort the results files** |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
86 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
87 You can sort the result file if you wish, it can help you to check results. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
88 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
89 In order to do so : enter the column to be used, all columns will be sorted according to the one filled in. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
90 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
91 Rows stay intact, just in different order like excel. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
92 You can also choose ascending or descending order, by default descending order is set. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
93 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
94 ------------------------------------------------------- |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
95 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
96 **Output** |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
97 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
98 The tool will produce 2 output files. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
99 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
100 * A text file containing the resulting filtered input file. |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
101 |
a55e8b137c6b
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
proteore
parents:
diff
changeset
|
102 * A text file containing the rows removed from the input file. |