Mercurial > repos > melpetera > generic_filter

comparison GalFilter/generic_filter.xml @ 3:cfd7c4aa5c26 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author melpetera
date Fri, 03 Jan 2020 04:09:28 -0500
parents 12cf1eed21f4
children
comparison
equal deleted inserted replaced
2:12cf1eed21f4 3:cfd7c4aa5c26
1 <tool id="generic_filter" name="Generic_Filter" version="2017.06"> 1 <tool id="generic_filter" name="Generic_Filter" version="2020.01">
2 <description>Removes elements according to numerical or qualitative values</description> 2 <description>Removes elements according to numerical or qualitative values</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1_4">r-batch</requirement> 4 <requirement type="package" version="1.1_4">r-batch</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
140 140
141 <help> 141 <help>
142 142
143 .. class:: infomark 143 .. class:: infomark
144 144
145 **Authors** Marion Landi and Melanie Petera 145 **Authors:**
146 Melanie Petera for original R code - Marion Landi and Melanie Petera for original Galaxy wrapper
147 **Maintainer:** Melanie Petera (PFEM - INRAE - MetaboHUB)
146 148
147 --------------------------------------------------- 149 ---------------------------------------------------
148 150
149 ============== 151 ==============
150 Generic_Filter 152 Generic Filter
151 ============== 153 ==============
152 154
153 ----------- 155 -----------
154 Description 156 Description
155 ----------- 157 -----------
162 Workflow position 164 Workflow position
163 ----------------- 165 -----------------
164 166
165 167
166 .. image:: filter.png 168 .. image:: filter.png
167 :width: 800 169 :width: 700
168 170
169 171
170 172
171 ----------- 173 -----------
172 Input files 174 Input files
173 ----------- 175 -----------
174 176
175 +----------------------------+------------+ 177 +----------------------------+------------+
176 | Parameter : num + label | Format | 178 | Parameter : num + label | Format |
177 +============================+============+ 179 +============================+============+
178 | 1 : Data Matrix file | tabular | 180 | 1 : Data matrix file | tabular |
179 +----------------------------+------------+ 181 +----------------------------+------------+
180 | 2 : Sample metadata file | tabular | 182 | 2 : Sample metadata file | tabular |
181 +----------------------------+------------+ 183 +----------------------------+------------+
182 | 3 : Variable metadata file | tabular | 184 | 3 : Variable metadata file | tabular |
183 +----------------------------+------------+ 185 +----------------------------+------------+
192 194
193 Deleting samples and/or variables according to Numerical values: 195 Deleting samples and/or variables according to Numerical values:
194 | If 'yes' (not default): execution deletes all samples or variables (according to selection) for which the designated 196 | If 'yes' (not default): execution deletes all samples or variables (according to selection) for which the designated
195 | numerical parameter ("Name of the column to remove" field) equals the selected range of values (depending on the "Interval of values to remove" chosen). 197 | numerical parameter ("Name of the column to remove" field) equals the selected range of values (depending on the "Interval of values to remove" chosen).
196 | To delete multiple independent intervals of value from the same parameter, it is necessary to add as many times as necessary 198 | To delete multiple independent intervals of value from the same parameter, it is necessary to add as many times as necessary
197 | the corresponding column via the button "Add new Identify the parameter to filter". 199 | the corresponding column via the "Insert Identify the parameter to filter" button.
198 200
199 | *On file (only if 'yes')* 201 | *On file (only if 'yes')*
200 | Choice between sample and variable filtering (referring to the input file containing the factor). 202 | Choice between sample and variable filtering (referring to the input file containing the factor).
201 | 203 |
202 204
216 | Numerical value(s) used as threshold, depending on the type of interval chosen above. 218 | Numerical value(s) used as threshold, depending on the type of interval chosen above.
217 | Only one value for 'lower' and 'upper'; two values for 'between' and 'extremity'. 219 | Only one value for 'lower' and 'upper'; two values for 'between' and 'extremity'.
218 | 220 |
219 221
220 | *Notes:* 222 | *Notes:*
221 | - these parameters can be used several times using the "Add new Identify the parameter to filter" button 223 | - these parameters can be used several times using the "Insert Identify the parameter to filter" button
222 | - Numerical filter does not remove NA values; if you want to suppress them, use the Qualitative filter below 224 | - Numerical filter does not remove NA values; if you want to suppress them, use the Qualitative filter below
223 | 225 |
224 226
225 227
226 Deleting samples and/or variables according to Qualitative values 228 Deleting samples and/or variables according to Qualitative values
227 | If 'yes' (not default): execution deletes all data samples or variables (according to selection) for which the designated 229 | If 'yes' (not default): execution deletes all data samples or variables (according to selection) for which the designated
228 | factor ("Name of the column to remove" field) equals the selected level ("Remove factor when" field). 230 | factor ("Name of the column to remove" field) equals the selected level ("Remove factor when" field).
229 | To delete multiple values of the same factor, it is necessary to add as many times as necessary the corresponding factor 231 | To delete multiple values of the same factor, it is necessary to add as many times as necessary the corresponding factor
230 | via the button "Add new Removing a level in factor". 232 | via the "Insert Removing a level in factor" button.
231 233
232 | *On file (only if 'yes')* 234 | *On file (only if 'yes')*
233 | Choice between sample and variable filtering (referring to the input file containing the factor). 235 | Choice between sample and variable filtering (referring to the input file containing the factor).
234 | 236 |
235 237
241 | Value that you want to delete from the selected column. 243 | Value that you want to delete from the selected column.
242 | Each line with that value of designated factor will be deleted. 244 | Each line with that value of designated factor will be deleted.
243 | 245 |
244 246
245 | *Notes:* 247 | *Notes:*
246 | - these parameters can be used several times using the "Add new Removing a level in factor" button 248 | - these parameters can be used several times using the "Insert Removing a level in factor" button
247 | - this filter can be used to filter NA in numerical parameters, or to remove a specific numerical value 249 | - this filter can be used to filter NA in numerical parameters, or to remove a specific numerical value
248 | 250 |
249 251
250 252
251 ------------ 253 ------------
253 ------------ 255 ------------
254 256
255 257
256 dataMatrix 258 dataMatrix
257 | tabular output 259 | tabular output
258 | Identical to the input Data Matrix file with the sample columns and variable lines deleted according to specified filters 260 | Identical to the input Data matrix file with the sample columns and variable lines deleted according to specified filters
259 | 261 |
260 262
261 sampleMetadata 263 sampleMetadata
262 | tabular output 264 | tabular output
263 | Identical to the input Sample metadata file with the sample lines deleted according to specified filters 265 | Identical to the input Sample metadata file with the sample lines deleted according to specified filters
269 | 271 |
270 272
271 273
272 --------------------------------------------------- 274 ---------------------------------------------------
273 275
274 --------------- 276 ----------------------
275 Working example 277 Additional information
276 --------------- 278 ----------------------
277 279
278 280
279 .. class:: warningmark 281 .. class:: warningmark
280 282
281 Soon see the corresponding "Page" 283 For more information about input files, refer to the corresponding "W4M HowTo" page:
284 | `W4M table format for Galaxy &lt;http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf&gt;`_
285 |
286
287
282 288
283 </help> 289 </help>
284 <citations> 290 <citations>
285 <citation type="doi">10.1093/bioinformatics/btu813</citation> 291 <citation type="doi">10.1093/bioinformatics/btu813</citation>
286 </citations> 292 </citations>