Mercurial > repos > melpetera > generic_filter
comparison GalFilter/generic_filter.xml @ 3:cfd7c4aa5c26 draft default tip
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 <http://workflow4metabolomics.org/sites/workflow4metabolomics.org/files/files/w4m_TableFormatForGalaxy_150908.pdf>`_ | |
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> |