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comparison freyja_aggregate_plot.xml @ 1:1f89eeba299a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
author iuc
date Fri, 07 Jul 2023 05:51:06 +0000
parents 0ceb9fb0f4ce
children
comparison
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0:0ceb9fb0f4ce 1:1f89eeba299a
69 <option value="D">day bins</option> 69 <option value="D">day bins</option>
70 </param> 70 </param>
71 </when> 71 </when>
72 <when value="no"/> 72 <when value="no"/>
73 </conditional> 73 </conditional>
74 <expand macro="plot_lineages"/>
75 <expand macro="plot_mincov"/>
74 </when> 76 </when>
75 <when value="dash"> 77 <when value="dash">
76 <param name="csv_meta" type="data" format="csv" 78 <param name="csv_meta" type="data" format="csv"
77 label="Provide sample(s) metadata file" 79 label="Provide sample(s) metadata file"
78 help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/> 80 help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/>
79 <param name="plot_title" type="text" value="" optional="true" label="Title"/> 81 <param name="plot_title" type="text" value="" optional="true" label="Title"/>
80 <param name="plot_intro" type="text" value="" optional="true" label="Introduction"/> 82 <param name="plot_intro" type="text" value="" optional="true" label="Introduction"/>
83 <expand macro="plot_mincov"/>
81 </when> 84 </when>
82 <when value="plot_and_dash"> 85 <when value="plot_and_dash">
83 <param name="csv_meta" type="data" format="csv" 86 <param name="csv_meta" type="data" format="csv"
84 label="Provide sample(s)/time(s) metadata file" 87 label="Provide sample(s)/time(s) metadata file"
85 help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/> 88 help="See info box below to learn more about the form of meta-file. Accepts only CSV (.csv) files"/>
90 <param name="interval" type="select" label="Choose interval" display="radio" 93 <param name="interval" type="select" label="Choose interval" display="radio"
91 help="Used for pdf non-interactive plot."> 94 help="Used for pdf non-interactive plot.">
92 <option value="MS" selected="true">month bins</option> 95 <option value="MS" selected="true">month bins</option>
93 <option value="D">day bins</option> 96 <option value="D">day bins</option>
94 </param> 97 </param>
98 <expand macro="plot_lineages"/>
99 <expand macro="plot_mincov"/>
95 </when> 100 </when>
96 <when value="none"/> 101 <when value="none"/>
97 </conditional> 102 </conditional>
98 </inputs> 103 </inputs>
99 <outputs> 104 <outputs>
129 <conditional name="plot_format"> 134 <conditional name="plot_format">
130 <param name="choice" value="none"/> 135 <param name="choice" value="none"/>
131 </conditional> 136 </conditional>
132 <output name="aggregated" ftype="tabular"> 137 <output name="aggregated" ftype="tabular">
133 <assert_contents> 138 <assert_contents>
139 <has_n_columns n="6" />
134 <has_text text="summarized"/> 140 <has_text text="summarized"/>
135 <has_text text="abundances"/> 141 <has_text text="abundances"/>
136 <has_text text="B.1.617.2"/> 142 <has_text text="B.1.617.2"/>
137 </assert_contents> 143 </assert_contents>
138 </output> 144 </output>
146 <conditional name="plot_format"> 152 <conditional name="plot_format">
147 <param name="choice" value="dash"/> 153 <param name="choice" value="dash"/>
148 <param name="csv_meta" value="csv_sample_meta.csv"/> 154 <param name="csv_meta" value="csv_sample_meta.csv"/>
149 <param name="plot_title" value="This is title"/> 155 <param name="plot_title" value="This is title"/>
150 <param name="plot_intro" value="Local WW Dashboard"/> 156 <param name="plot_intro" value="Local WW Dashboard"/>
157 <param name="mincov" value="75"/>
151 </conditional> 158 </conditional>
152 <output name="abundances_dashboard" ftype="html"> 159 <output name="abundances_dashboard" ftype="html">
153 <assert_contents> 160 <assert_contents>
154 <has_text text="Local WW Dashboard"/> 161 <has_text text="Local WW Dashboard"/>
155 </assert_contents> 162 </assert_contents>
167 <param name="choice" value="yes"/> 174 <param name="choice" value="yes"/>
168 <param name="csv_meta" value="times_metadata.csv"/> 175 <param name="csv_meta" value="times_metadata.csv"/>
169 <param name="interval" value="D"/> 176 <param name="interval" value="D"/>
170 </conditional> 177 </conditional>
171 </conditional> 178 </conditional>
179 <param name="lineages" value="true"/>
172 <output name="abundances_plot" ftype="pdf"> 180 <output name="abundances_plot" ftype="pdf">
173 <assert_contents> 181 <assert_contents>
174 <has_text text="Matplotlib"/> 182 <has_text text="Matplotlib"/>
175 </assert_contents> 183 </assert_contents>
176 </output> 184 </output>
182 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/> 190 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/>
183 </conditional> 191 </conditional>
184 <conditional name="plot_format"> 192 <conditional name="plot_format">
185 <param name="choice" value="dash"/> 193 <param name="choice" value="dash"/>
186 <param name="csv_meta" value="csv_sample_meta2.csv"/> 194 <param name="csv_meta" value="csv_sample_meta2.csv"/>
187 <param name="plot_title" value="This is title"/> 195 <param name="plot_title" value="Title"/>
188 <param name="plot_intro" value="Local WW Dashboard"/> 196 <param name="plot_intro" value="Dashboard"/>
189 </conditional> 197 </conditional>
190 <output name="aggregated" ftype="tabular"> 198 <output name="aggregated" ftype="tabular">
191 <assert_contents> 199 <assert_contents>
200 <has_n_columns n="6" />
192 <has_text text="summarized"/> 201 <has_text text="summarized"/>
193 <has_text text="abundances"/>
194 <has_text text="B.1.617.2"/>
195 </assert_contents> 202 </assert_contents>
196 </output> 203 </output>
197 <output name="abundances_dashboard" ftype="html"> 204 <output name="abundances_dashboard" ftype="html">
198 <assert_contents> 205 <assert_contents>
199 <has_text text="Local WW Dashboard"/> 206 <has_text text="Dashboard"/>
200 </assert_contents> 207 </assert_contents>
201 </output> 208 </output>
202 </test> 209 </test>
203 <!-- Test 05: aggregate and plot commands --> 210 <!-- Test 05: aggregate and plot commands -->
204 <test expect_num_outputs="2"> 211 <test expect_num_outputs="2">
214 <param name="interval" value="D"/> 221 <param name="interval" value="D"/>
215 </conditional> 222 </conditional>
216 </conditional> 223 </conditional>
217 <output name="aggregated" ftype="tabular"> 224 <output name="aggregated" ftype="tabular">
218 <assert_contents> 225 <assert_contents>
226 <has_n_columns n="6" />
219 <has_text text="summarized"/> 227 <has_text text="summarized"/>
220 <has_text text="abundances"/> 228 <has_text text="abundances"/>
221 <has_text text="B.1.617.2"/> 229 <has_text text="B.1.617.2"/>
222 </assert_contents> 230 </assert_contents>
223 </output> 231 </output>
234 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/> 242 <param name="demix_file" value="abundances.tsv,abundances2.tsv,abundances3.tsv"/>
235 </conditional> 243 </conditional>
236 <conditional name="plot_format"> 244 <conditional name="plot_format">
237 <param name="choice" value="plot_and_dash"/> 245 <param name="choice" value="plot_and_dash"/>
238 <param name="csv_meta" value="csv_sample_meta2.csv"/> 246 <param name="csv_meta" value="csv_sample_meta2.csv"/>
239 <param name="plot_title" value="This is title"/> 247 <param name="plot_title" value="Title"/>
240 <param name="plot_intro" value="Local WW Dashboard"/> 248 <param name="plot_intro" value="Dashboard"/>
241 <param name="interval" value="D"/> 249 <param name="interval" value="D"/>
242 </conditional> 250 </conditional>
243 <output name="aggregated" ftype="tabular"> 251 <output name="aggregated" ftype="tabular">
244 <assert_contents> 252 <assert_contents>
253 <has_n_columns n="6" />
245 <has_text text="summarized"/> 254 <has_text text="summarized"/>
246 <has_text text="abundances"/>
247 <has_text text="B.1.617.2"/>
248 </assert_contents> 255 </assert_contents>
249 </output> 256 </output>
250 <output name="abundances_plot" ftype="pdf"> 257 <output name="abundances_plot" ftype="pdf">
251 <assert_contents> 258 <assert_contents>
252 <has_text text="Matplotlib"/> 259 <has_text text="Matplotlib"/>
253 </assert_contents> 260 </assert_contents>
254 </output> 261 </output>
255 <output name="abundances_dashboard" ftype="html"> 262 <output name="abundances_dashboard" ftype="html">
256 <assert_contents> 263 <assert_contents>
257 <has_text text="Local WW Dashboard"/> 264 <has_text text="Dash"/>
258 </assert_contents> 265 </assert_contents>
259 </output> 266 </output>
260 </test> 267 </test>
261 </tests> 268 </tests>
262 <help><![CDATA[ 269 <help><![CDATA[
263 @HELP_HEADER@ 270 @HELP_HEADER@
264 271
265 Information about **freyja aggregate** method 272 Information about **freyja aggregate** method
266 ============================================= 273 =============================================
267 274
268 Method for manipulating the "demixed" output files. 275 Method for manipulating the "demixed" output files.
269 276
270 Outputs 277 Outputs
271 ------- 278 -------
272 279
273 This resulting aggregated data can analyzed directly as a tsv file, or can be visualized using *freyja plot* and *freyja dash*. 280 This resulting aggregated data can analyzed directly as a tsv file, or can be visualized using *freyja plot* and *freyja dash*.
275 Information about **freyja plot** method 282 Information about **freyja plot** method
276 ======================================== 283 ========================================
277 284
278 Method provides a fractional abundance estimate for all aggregated samples. 285 Method provides a fractional abundance estimate for all aggregated samples.
279 286
280 A **time(s) metadata CSV file** should have this form: 287 A **time(s) metadata CSV file** should have *Sample,sample_collection_datetime* form:
281 288
282 *Sample,sample_collection_datetime* 289 *sample_0.tsv,03/01/21*
283 290
284 *sample_0.tsv,03/01/21* 291 *sample_1.tsv,03/03/21*
285 292
286 *sample_1.tsv,03/03/21* 293 *sample_2.tsv,03/08/21*
287 294
288 *sample_2.tsv,03/08/21* 295 *sample_3.tsv,03/10/21*
289 296
290 *sample_3.tsv,03/10/21* 297 or *Sample,sample_collection_datetime,viral_load* form:
291 298
292 *sample_4.tsv,03/12/21* 299 *sample_0.tsv,03/01/21,460326*
293 300
294 *sample_5.tsv,03/14/21* 301 *sample_1.tsv,03/03/21,176645.1*
295 302
296 *sample_6.tsv,03/17/21* 303 *sample_2.tsv,03/08/21,449891.7*
297 304
298 *sample_7.tsv,03/20/21* 305 *sample_3.tsv,03/10/21,361699.5*
299 306
300 *sample_8.tsv,03/25/21* 307
301 308 Note: sample_collection_datetime can have either *MM/DD/YY* or *YYYY-MM-DD* format.
302 *sample_9.tsv,03/30/21*
303
304 *sample_10.tsv,03/31/21*
305
306 *sample_11.tsv,04/04/21*
307 309
308 310
309 Information about **freyja dash** method 311 Information about **freyja dash** method
310 ======================================== 312 ========================================
311 313
312 Functionality to rapidly prepare a dashboard web page, directly from aggregated freyja output. 314 Functionality to rapidly prepare a dashboard web page, directly from aggregated freyja output.
313 315
314 A **sample(s) metadata CSV file** should have this form: 316 A **sample(s) metadata CSV file** should have this form:
315 317
316 *Sample,sample_collection_datetime,viral_load* 318 *Sample,sample_collection_datetime,viral_load*
317 319
318 *sample_0.tsv,03/01/21,460326* 320 *sample_0.tsv,03/01/21,460326*
319 321
320 *sample_1.tsv,03/03/21,176645.1* 322 *sample_1.tsv,03/03/21,176645.1*
321 323
322 *sample_2.tsv,03/08/21,449891.7* 324 *sample_2.tsv,03/08/21,449891.7*
323 325
324 *sample_3.tsv,03/10/21,361699.5* 326 *sample_3.tsv,03/10/21,361699.5*
325 327
326 *sample_4.tsv,03/12/21,658923.9* 328
327 329 Note: sample_collection_datetime can have either *MM/DD/YY* or *YYYY-MM-DD* format.
328 *sample_5.tsv,03/14/21,500432.8*
329
330 *sample_6.tsv,03/17/21,791406.4*
331
332 *sample_7.tsv,03/20/21,628119.9*
333
334 *sample_8.tsv,03/25/21,810673.9*
335
336 *sample_9.tsv,03/30/21,1263564.4*
337
338 *sample_10.tsv,03/31/21,1627556.3*
339
340 *sample_11.tsv,04/04/21,1528006.4*
341 330
342 331
343 ]]></help> 332 ]]></help>
344 <expand macro="citations"/> 333 <expand macro="citations"/>
345 </tool> 334 </tool>