Mercurial > repos > proteore > proteore_filter_keywords_values

comparison filter_kw_val.xml @ 2:52a7afd01c6d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9af2cf12c26c94e7206751ccf101a3368f92d0ba
author proteore
date Tue, 18 Dec 2018 09:25:11 -0500
parents cb9555653b09
children 68cee865018e
comparison
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1:cb9555653b09 2:52a7afd01c6d
1 <tool id="MQoutputfilter" name="Filter by keywords or numerical value" version="2018.09.21"> 1 <tool id="MQoutputfilter" name="Filter by keywords and/or numerical value" version="2018.12.18">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 </requirements> 4 </requirements>
5 <stdio> 5 <stdio>
6 <exit_code range="1:" /> 6 <exit_code range="1:" />
16 #for $key in $keyword 16 #for $key in $keyword
17 #if $key.k.kw != "None" 17 #if $key.k.kw != "None"
18 #if $key.k.kw == "text" 18 #if $key.k.kw == "text"
19 --kw "$key.k.txt" "$key.ncol" "$key.match" 19 --kw "$key.k.txt" "$key.ncol" "$key.match"
20 #else if $key.k.kw == "file" 20 #else if $key.k.kw == "file"
21 --kw_file "$key.k.file" "$key.ncol" "$key.match" 21 --kw_file "$key.k.file" "$key.k.header" "$key.k.ncol" "$key.ncol" "$key.match"
22 #end if 22 #end if
23 #end if 23 #end if
24 #end for 24 #end for
25 25
26 ## value to filter 26 ## value to filter
54 --sort_col "$sort_column,$reversed_sort" 54 --sort_col "$sort_column,$reversed_sort"
55 #end if 55 #end if
56 56
57 ]]></command> 57 ]]></command>
58 <inputs> 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" /> 59 <param type="data" name="input1" format="txt,tabular" label="Input file" />
60 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 60 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
61 <param name="operator" type="select" label="Please select an operator to combine your filters (if more than one)" help="OR : only one filter must be satisfied to filter a row, AND : all your filters must be satisfied to filter a row" > 61 <param name="operator" type="select" label="Select an operator to combine your filters (if more than one)" 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> 62 <option value="OR" selected="True">OR</option>
63 <option value="AND">AND</option> 63 <option value="AND">AND</option>
64 </param> 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." /> 65
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" > 66 <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' /> 67 <param name="ncol" type="text" value="c1" label="Column number on which 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' /> 68 <param type="boolean" name="match" truevalue="True" label="Search for exact match?" help='Choosing "Yes" will only filter out exact match (e.g. case sensitive), see help section' />
70 <conditional name="k" > 69 <conditional name="k" >
71 <param argument="--kw" type="select" label="Filter by keyword" > 70 <param name="kw" type="select" label="Enter keywords" >
72 <option value="text" selected="true">Enter keywords (copy/paste)</option> 71 <option value="text" selected="true">copy/paste</option>
73 <option value="file">Choose a file containing keywords</option> 72 <option value="file">File containing keywords</option>
74 </param> 73 </param>
75 <when value="None" />
76 <when value="text" > 74 <when value="text" >
77 <param name="txt" type="text" label="Copy/paste keywords to be filtered out" help='Keywords must be separated by ";", for example: A8K2U0;Q5TA79;O43175' > 75 <param name="txt" type="text" label="Copy/paste keywords to be filtered out" help='Keywords must be separated by tab, space or carriage return into the form field, for example: A8K2U0 Q5TA79 O43175' >
78 <sanitizer> 76 <sanitizer>
79 <valid initial="string.printable"> 77 <valid initial="string.printable">
80 <remove value="&apos;"/> 78 <remove value="&apos;"/>
81 </valid> 79 </valid>
82 <mapping initial="none"> 80 <mapping initial="none">
84 </mapping> 82 </mapping>
85 </sanitizer> 83 </sanitizer>
86 </param> 84 </param>
87 </when> 85 </when>
88 <when value="file" > 86 <when value="file" >
89 <param name="file" type="data" format="txt,tabular" label="Choose a file containing keywords" /> 87 <param name="file" type="data" format="txt,tabular" label="File containing keywords" />
88 <param name="ncol" type="text" value="c1" label="Specify the column containing keywords" help='For example, fill in "c1" if keywords are in the first column' />
89 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
90 </when> 90 </when>
91 </conditional> 91 </conditional>
92 </repeat> 92 </repeat>
93 <repeat name="value" title="Filter by value" > 93 <repeat name="value" title="Filter by numerical value" >
94 <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' /> 94 <param name="ncol" type="text" value="c1" label="Column number on which to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' />
95 <conditional name="v" > 95 <conditional name="v" >
96 <param argument="--val" type="select" label="Filter by value" > 96 <param argument="Numerical Value" type="select" label="Select operator" >
97 <option value="None">---</option>
98 <option value="Equal">=</option> 97 <option value="Equal">=</option>
99 <option value="Higher">&gt;</option> 98 <option value="Higher">&gt;</option>
100 <option value="Equal or higher">&gt;=</option> 99 <option value="Equal or higher">&gt;=</option>
101 <option value="Lower">&lt;</option> 100 <option value="Lower">&lt;</option>
102 <option value="Equal or lower">&lt;=</option> 101 <option value="Equal or lower">&lt;=</option>
103 <option value="Different">!=</option> 102 <option value="Different">!=</option>
104 </param> 103 </param>
105 <when value="None" >
106 </when>
107 <when value="Equal" > 104 <when value="Equal" >
108 <param name="equal" type="float" value="" label="Value" /> 105 <param name="equal" type="float" value="" label="Value" />
109 </when> 106 </when>
110 <when value="Higher" > 107 <when value="Higher" >
111 <param type="float" name="higher" value="" label="Value" /> 108 <param type="float" name="higher" value="" label="Value" />
122 <when value="Different"> 119 <when value="Different">
123 <param type="float" name="different" value="" label="Value"/> 120 <param type="float" name="different" value="" label="Value"/>
124 </when> 121 </when>
125 </conditional> 122 </conditional>
126 </repeat> 123 </repeat>
127 <repeat name="values_range" title="Filter by range of values"> 124 <repeat name="values_range" title="Filter by range of numerical values">
128 <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' /> 125 <param name="ncol" type="text" value="c1" label="Column number on which to apply the filter" help='For example, fill in "c1" if the keywords you want to filter out are listed in the first column' />
129 <param name="bottom_value" type="float" value="" label="Please enter the bottom value" /> 126 <param name="bottom_value" type="float" value="" label="Enter the bottom value" />
130 <param name="top_value" type="float" value="" label="Please enter the top value" /> 127 <param name="top_value" type="float" value="" label="Enter the top value" />
131 <param name="inclusive" type="boolean" label="inclusive range ?" checked="false" truevalue="true" falsevalue="false" /> 128 <param name="inclusive" type="boolean" label="inclusive range ?" checked="false" truevalue="true" falsevalue="false" />
132 </repeat> 129 </repeat>
133 </inputs> 130 <param name="sort_column" type="text" value="" label="Sort result files by:" help="Fill in 'c1' if you want to sort your result file by the column 1 values" />
131 <param name="reversed_sort" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Sort in descending order ?"/>
132 </inputs>
134 <outputs> 133 <outputs>
135 <data name="output1" format="tabular" label="${tool.name} on ${input1.name}" /> 134 <data name="output1" format="tsv" label="${tool.name} on ${input1.name}" />
136 <data name="filtered_file" format="tabular" label="${tool.name} on ${input1.name} - Filtered lines" /> 135 <data name="filtered_file" format="tsv" label="${tool.name} on ${input1.name} - Filtered lines" />
137 </outputs> 136 </outputs>
138 <tests> 137 <tests>
139 <test> 138 <test>
140 <param name="input1" value="Lacombe_et_al_2017_OK.txt" /> 139 <param name="input1" value="Lacombe_et_al_2017_OK.txt" />
141 <param name="header" value="true" /> 140 <param name="header" value="true" />
145 <repeat name="keyword"> 144 <repeat name="keyword">
146 <param name="ncol" value="c1" /> 145 <param name="ncol" value="c1" />
147 <param name="match" value="True" /> 146 <param name="match" value="True" />
148 <conditional name="k"> 147 <conditional name="k">
149 <param name="kw" value="text" /> 148 <param name="kw" value="text" />
150 <param name="txt" value="P04264;P35908;P13645;Q5D862;Q5T749;Q8IW75;P81605;P22531;P59666;P78386" /> 149 <param name="txt" value="P04264 P35908 P13645 Q5D862 Q5T749 Q8IW75 P81605 P22531 P59666 P78386" />
151 </conditional> 150 </conditional>
152 </repeat> 151 </repeat>
153 <repeat name="value"> 152 <repeat name="value">
154 <param name="ncol" value="c3"/> 153 <param name="ncol" value="c3"/>
155 <conditional name="v"> 154 <conditional name="v">
160 <output name="output1" file="output.csv" /> 159 <output name="output1" file="output.csv" />
161 <output name="filtered_file" file="filtered_output.csv" /> 160 <output name="filtered_file" file="filtered_output.csv" />
162 </test> 161 </test>
163 </tests> 162 </tests>
164 <help><![CDATA[ 163 <help><![CDATA[
165 This tool allows to remove unneeded data (e.g. contaminants, non-significant values) from a proteomics results file (e.g. MaxQuant or Proline output). 164 **Description**
165
166 This tool allows to filter out data according to different criteria such as keywords (e.g. a list of contaminants) or numerical values (e.g. intensity measurements below a given threshold).
167 A boolean operator "OR/AND" allows to combine different type of filters making this tool very powerful.
168
169 -----
170
171 **Input**
172
173 A table (file in txt, tab, tsv, csv format) of your identification and/or quantification results for example.
174
175 -----
176
177 **Parameters**
178
179 **AND/OR operator**
180
181 As many filters as needed can be combined, you can choose how filters apply on your data by using the following boolean operators:
182
183 - OR: only one filter must be satisfied to remove one row
184 - AND: all filters must be satisfied to remove one row
185
186 -----
166 187
167 **Filter by keyword(s)** 188 **Filter by keyword(s)**
168 189
169 Several options can be used. For each option, you can fill in the field or upload a file which contains the keywords. 190 Click on the "Filter by keywords" box to use it. You can either fill in the field (copy/paste) or upload a file which contains the keywords.
170 191
171 - If you choose to fill in the field, the keywords should be separated by ";", for example: A8K2U0;Q5TA79;O43175 192 "Column number on which to apply the filter": You must then specify the column number of your input file on wich to apply the filter by keywords.
193
194 - If you choose to fill in the field, the keywords should be separated by tab, space or carriage return into the form field, for example: A8K2U0 Q5TA79 O43175
172 195
173 - If you choose to upload a file in a text format in which each line is a keyword, for example: 196 - If you choose to upload a file in a text format in which each line is a keyword, for example:
174 197
175 REV
176
177 TRYP_PIG 198 TRYP_PIG
178 199
179 ALDOA_RABBIT 200 ALDOA_RABBIT
180 201
181 **The line that contains these keywords will be eliminated from input file.** 202 LYSO_ECOLI
182 203
183 **Keywords search can be applied by performing either exact match or partial one by using the following option** 204 Lines that contains these keywords will be removed from input file.
205
206 "Search for exact match?": Keywords search can be applied by performing either exact match or partial one by using the following option:
184 207
185 - If you choose **Yes**, only the fields that contains exactly the same content will be removed. 208 - If you choose **Yes**, only the fields that contains exactly the same content will be removed.
186 209
187 - If you choose **No**, all the fields containing the keyword will be removed. 210 - If you choose **No**, all the fields containing the keyword will be removed.
188 211
189 For example: 212 Example:
190 213
191 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly "kinase" is removed. 214 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly the word "kinase" will be removed.
192 215
193 **No** option (partial match) for "kinase": not only lines which contain "kinase" but also lines with "alpha-kinase" (and so on) are removed. 216 **No** option (partial match) for "kinase": lines which contain "kinase" and lines with "alpha-kinase" (and so on) will be removed.
194 217
195 ----- 218 -----
196 219
197 **Filter by values** 220 **Filter by numerical values**: You can filter your data by a column of numerical values.
198 221
199 You can filter your data by a column of numerical values. 222 "Column number on which to apply the filter": you must specify the column number of your input file on wich to apply the filter by numerical value.
200 Enter the column to be use and select one operator in the list : 223
201 224 Then select one of the operators in the list :
202 - = 225
203 - != 226 - = (equal)
204 - < 227 - != (not equal)
205 - <= 228 - < (lower than)
206 - > 229 - <= (lower than or equal to)
207 - >= 230 - > (greater than)
208 231 - >= (greater than or equal to)
209 Then enter the value to filter and specify the column to apply that option. 232
210 If a row contains a value that correspond to your settings, it will be filtered. 233 Then enter the numerical threshold to apply by filling the "Value" box.
211 234 If you choose > 10, each row containing a numerical value (in the chosen column of your input file) that correspond to your settings will be filtered out.
212 ----- 235
213 236 -----
214 **Filter by a range of values** 237
215 238 **Filter by a range of values**: You can also set a range of values to filter your file.
216 You can also set a range of values to filter your file. 239 Conversely to the numeric filter, rows with numerical values within the defined range will be kept while rows with values out of this range will be filtered out.
217 In opposition to value filter, rows with values inside of the defined range are kept. 240
218 241 -----
219 Rows with values outside of the defined range will be filtered. 242
220 243 **Sort results files**
221 ----- 244
222 245 You can sort your results by column in ascending (default value) or descending by entering the column number on which to sort the data.
223 **AND/OR operator**
224
225 Since you can add as many filters as you want, you can choose how filters apply on your data.
226
227 AND or OR operator option works on all filters :
228
229 - OR : only one filter to be satisfied to remove one row
230 - AND : all filters must be satisfied to remove one row
231
232 -----
233
234 **Sort the results files**
235
236 You can sort the result file if you wish, it can help you to check results.
237
238 In order to do so : enter the column to be used, all columns will be sorted according to the one filled in.
239
240 Rows stay intact, just in different order like excel.
241 You can also choose ascending or descending order, by default ascending order is set.
242 246
243 ----- 247 -----
244 248
245 **Output** 249 **Output**
246 250
247 The tool will produce 2 output files. 251 The tool returns two output files.
248 252
249 * A text file containing the resulting filtered input file. 253 * A text file containing the results that pass your filters
250 254
251 * A text file containing the rows removed from the input file. 255 * A text file containing the rows removed from the input file (i.e. containing data taht do not pass your filter(s).
252 256
253 ----- 257 -----
254 258
255 .. class:: infomark 259 .. class:: infomark
256 260