Mercurial > repos > proteore > proteore_filter_keywords_values

comparison filter_kw_val.xml @ 0:a55e8b137c6b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 688c456ca57914a63c20eba942ec5fe81e896099-dirty
author proteore
date Wed, 19 Sep 2018 05:01:15 -0400
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1 <tool id="MQoutputfilter" name="Filter by keywords or numerical value" version="2018.08.22">
2 <description></description>
3 <requirements>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8 <command><![CDATA[
9 python $__tool_directory__/filter_kw_val.py
10 -i "$input1,$header"
11 -o "$output1"
12 --filtered_file "$filtered_file"
13 --operator "$operator"
14
15 ## Keywords
16 #for $key in $keyword
17 #if $key.k.kw != "None"
18 #if $key.k.kw == "text"
19 --kw "$key.k.txt" "$key.ncol" "$key.match"
20 #else if $key.k.kw == "file"
21 --kw_file "$key.k.file" "$key.ncol" "$key.match"
22 #end if
23 #end if
24 #end for
25
26 ## value to filter
27 #for $val in $value
28 #if $val.v.val != "None"
29 --value
30 #if $val.v.val == "Equal"
31 $val.v.equal "$val.ncol" "="
32 #else if $val.v.val == "Higher"
33 $val.v.higher "$val.ncol" ">"
34 #else if $val.v.val == "Equal or higher"
35 $val.v.equal_higher "$val.ncol" ">="
36 #else if $val.v.val == "Lower"
37 $val.v.lower "$val.ncol" "<"
38 #else if $val.v.val == "Equal or lower"
39 $val.v.equal_lower "$val.ncol" "<="
40 #else
41 $val.v.different "$val.ncol" "!="
42 #end if
43 #end if
44 #end for
45
46 ##range of values to keep
47 #for $vr in $values_range
48 #if vr
49 --values_range $vr.bottom_value $vr.top_value $vr.ncol $vr.inclusive
50 #end if
51 #end for
52
53 #if $sort_column != ""
54 --sort_col "$sort_column,$reversed_sort"
55 #end if
56
57 ]]></command>
58 <inputs>
59 <param type="data" name="input1" format="txt,tabular" label="Input file" help="Input file is a tab-delimited file containing proteomics identification and/or quantitative results" />
60 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
61 <param name="operator" type="select" label="Please select an operator for your filters" help="OR : only one filter must be satisfied to filter a row, AND : all your filters must be satisfied to filter a row" >
62 <option value="OR" selected="True">OR</option>
63 <option value="AND">AND</option>
64 </param>
65 <param name="sort_column" type="text" value="" label="If you want to sort the result files by values from a column, please enter a column number" help="For example : fill in 'c1' if you want to sort your result file by the column 1 values." />
66 <param name="reversed_sort" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Sort in descending order ?"/>
67 <repeat name="keyword" title="Filter by keywords" >
68 <param name="ncol" type="text" value="c1" label="Please specify the column number of the input file on which you want to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' />
69 <param type="boolean" name="match" truevalue="True" label="Would you like to search for exact match?" help='Choosing "Yes" will only filter out exact match (i.e. case sensitive), see below for more details' />
70 <conditional name="k" >
71 <param argument="--kw" type="select" label="Filter by keyword" >
72 <option value="None" selected="True">---</option>
73 <option value="text">Enter keywords (copy/paste)</option>
74 <option value="file">Choose a file containing keywords</option>
75 </param>
76 <when value="None" />
77 <when value="text" >
78 <param name="txt" type="text" label="Copy/paste keywords to be filtered out" help='Keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175' >
79 <sanitizer>
80 <valid initial="string.printable">
81 <remove value="&apos;"/>
82 </valid>
83 <mapping initial="none">
84 <add source="&apos;" target="__sq__"/>
85 </mapping>
86 </sanitizer>
87 </param>
88 </when>
89 <when value="file" >
90 <param name="file" type="data" format="txt,tabular" label="Choose a file containing keywords" />
91 </when>
92 </conditional>
93 </repeat>
94 <repeat name="value" title="Filter by value" >
95 <param name="ncol" type="text" value="c1" label="Please specify the column number of the input file on which you want to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' />
96 <conditional name="v" >
97 <param argument="--val" type="select" label="Filter by value" >
98 <option value="None">---</option>
99 <option value="Equal">=</option>
100 <option value="Higher">&gt;</option>
101 <option value="Equal or higher">&gt;=</option>
102 <option value="Lower">&lt;</option>
103 <option value="Equal or lower">&lt;=</option>
104 <option value="Different">!=</option>
105 </param>
106 <when value="None" >
107 </when>
108 <when value="Equal" >
109 <param name="equal" type="float" value="" label="Value" />
110 </when>
111 <when value="Higher" >
112 <param type="float" name="higher" value="" label="Value" />
113 </when>
114 <when value="Equal or higher" >
115 <param type="float" name="equal_higher" value="" label="Value" />
116 </when>
117 <when value="Lower" >
118 <param type="float" name="lower" value="" label="Value" />
119 </when>
120 <when value="Equal or lower" >
121 <param type="float" name="equal_lower" value="" label="Value" />
122 </when>
123 <when value="Different">
124 <param type="float" name="different" value="" label="Value"/>
125 </when>
126 </conditional>
127 </repeat>
128 <repeat name="values_range" title="Filter by range of values">
129 <param name="ncol" type="text" value="c1" label="Please specify the column number of the input file on which you want to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' />
130 <param name="bottom_value" type="float" value="" label="Please enter the bottom value" />
131 <param name="top_value" type="float" value="" label="Please enter the top value" />
132 <param name="inclusive" type="boolean" label="inclusive range ?" checked="false" truevalue="true" falsevalue="false" />
133 </repeat>
134 </inputs>
135 <outputs>
136 <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" />
137 <data name="filtered_file" format="tabular" label="${tool.name} on ${input1.name} - Filtered lines" />
138 </outputs>
139 <tests>
140 <test>
141 <param name="input1" value="Lacombe_et_al_2017_OK.txt" />
142 <param name="header" value="true" />
143 <param name="operator" value="OR"/>
144 <param name="sort_column" value="c1"/>
145 <param name="reversed_sort" value="false"/>
146 <repeat name="keyword">
147 <param name="ncol" value="c1" />
148 <param name="match" value="True" />
149 <conditional name="k">
150 <param name="kw" value="text" />
151 <param name="txt" value="P04264;P35908;P13645;Q5D862;Q5T749;Q8IW75;P81605;P22531;P59666;P78386" />
152 </conditional>
153 </repeat>
154 <repeat name="value">
155 <param name="ncol" value="c3"/>
156 <conditional name="v">
157 <param name="val" value="Higher"/>
158 <param name="higher" value="20" />
159 </conditional>
160 </repeat>
161 <output name="output1" file="output.csv" />
162 <output name="filtered_file" file="filtered_output.csv" />
163 </test>
164 </tests>
165 <help><![CDATA[
166 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output).
167
168 **Filter by keyword(s)**
169
170 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords.
171
172 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175
173
174 - If you choose to upload a file in a text format in which each line is a keyword, for example:
175
176 REV
177
178 TRYP_PIG
179
180 ALDOA_RABBIT
181
182 **The line that contains these keywords will be eliminated from input file.**
183
184 **Keywords search can be applied by performing either exact match or partial one by using the following option**
185
186 - If you choose **Yes**, only the fields that contains exactly the same content will be removed.
187
188 - If you choose **No**, all the fields containing the keyword will be removed.
189
190 For example:
191
192 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed.
193
194 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed.
195
196 -----
197
198 **Filter by values**
199
200 You can filter your data by a column of numerical values.
201 Enter the column to be use and select one operator in the list :
202
203 - =
204 - !=
205 - <
206 - <=
207 - >
208 - >=
209
210 Then enter the value to filter and specify the column to apply that option.
211 If a row contains a value that correspond to your settings, it will be filtered.
212
213 -----
214
215 **Filter by a range of values**
216
217 You can also set a range of values to filter your file.
218 In opposition to value filter, rows with values inside of the defined range are kept.
219
220 Rows with values outside of the defined range will be filtered.
221
222 -----
223
224 **AND/OR operator**
225
226 Since you can add as many filters as you want, you can choose how filters apply on your data.
227
228 AND or OR operator option works on all filters :
229
230 - OR : only one filter to be satisfied to remove one row
231 - AND : all filters must be satisfied to remove one row
232
233 -----
234
235 **Sort the results files**
236
237 You can sort the result file if you wish, it can help you to check results.
238
239 In order to do so : enter the column to be used, all columns will be sorted according to the one filled in.
240
241 Rows stay intact, just in different order like excel.
242 You can also choose ascending or descending order, by default ascending order is set.
243
244 -----
245
246 **Output**
247
248 The tool will produce 2 output files.
249
250 * A text file containing the resulting filtered input file.
251
252 * A text file containing the rows removed from the input file.
253
254 -----
255
256 .. class:: infomark
257
258 **Authors**
259
260 T.P. Lien Nguyen, David Christiany, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
261
262 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
263
264 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
265
266 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
267
268 ]]></help>
269 <citations>
270 </citations>
271 </tool>