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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit ec66b5b0627e7cf15b6e67e90d82ba8e0743b761
author galaxyp
date Mon, 18 Mar 2024 12:34:39 +0000
parents 9bf325045235
children
comparison
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6:eb811f3018ea 7:8bd7734309f6
1 <tool id="metaquantome_viz" name="metaQuantome: visualize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="metaquantome_viz" name="metaQuantome: visualize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>taxonomic analysis, functional analysis, and function-taxonomy analysis results</description> 2 <description>taxonomic analysis, functional analysis, and function-taxonomy analysis results</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <xml name="barcol"> 5 <xml name="barcol">
6 <param argument="--barcol" type="select" label="Color for the bar fill"> 6 <param argument="--barcol" type="select" label="Color for the bar fill">
7 <option value="1">Blue</option> 7 <option value="1">Blue</option>
8 <option value="2">Orange</option> 8 <option value="2">Orange</option>
9 <option value="3">Yellow</option> 9 <option value="3">Yellow</option>
10 <option value="4">Red</option> 10 <option value="4">Red</option>
11 <option value="5">Violet</option> 11 <option value="5">Violet</option>
12 <option value="6">Black</option> 12 <option value="6">Black</option>
13 <help> 13 <help>
14 These same colors are also used in the heatmap and PCA plot, 14 These same colors are also used in the heatmap and PCA plot,
15 so the colors can be tweaked to match. Note that these colors 15 so the colors can be tweaked to match. Note that these colors
16 are coded as 1 through 6 in the command line tool. 16 are coded as 1 through 6 in the command line tool.
17 </help> 17 </help>
18 </param> 18 </param>
19 </xml> 19 </xml>
20 <xml name="common_bar_params"> 20 <xml name="common_bar_params">
21 <param argument="--meancol" type="text" label="Mean intensity column name" 21 <param argument="--meancol" type="text" label="Mean intensity column name" help="Mean intensity column name for desired experimental condition">
22 help="Mean intensity column name for desired experimental condition"> 22 <validator type="empty_field"/>
23 <validator type="empty_field"/> 23 </param>
24 </param> 24 <param argument="--nterms" type="integer" value="5" min="1" optional="true" label="Number of terms to display" help="leave blank for all terms"/>
25 <param argument="--nterms" type="integer"
26 value="5" min="1" optional="true"
27 label="Number of terms to display"
28 help="leave blank for all terms"/>
29 </xml> 25 </xml>
30 <xml name="common_volc_params"> 26 <xml name="common_volc_params">
31 <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe"> 27 <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe">
32 <validator type="empty_field"/> 28 <validator type="empty_field"/>
33 </param> 29 </param>
34 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe"> 30 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
35 <validator type="empty_field"/> 31 <validator type="empty_field"/>
36 </param> 32 </param>
37 <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" 33 <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" help="Provides text annotatation for the plot. Optional. If missing, no text will be plotted."/>
38 help="Provides text annotatation for the plot. Optional. If missing, no text will be plotted."/> 34 <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false" label="Flip the fold change (i.e., multiply log fold change by -1)"/>
39 <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false"
40 label="Flip the fold change (i.e., multiply log fold change by -1)"/>
41 </xml> 35 </xml>
42 <xml name="common_heatmap_params"> 36 <xml name="common_heatmap_params">
43 <conditional name="heatmap"> 37 <conditional name="heatmap">
44 <param argument="--filter_to_sig" type="boolean" checked="false" 38 <param argument="--filter_to_sig" type="select" label="Only plot significant term" help="Necessitates use of results from `test`">
45 label="Only plot significant term" help="Necessitates use of results from `test`"/> 39 <option value="true">Only plot significant term</option>
46 <when value="true"> 40 <option value="false">Plot all terms</option>
47 <param argument="--alpha" type="float" 41 </param>
48 value="0.05" min="0.0" max="1.0" 42 <when value="true">
49 label="The q-value significance level"/> 43 <param argument="--alpha" type="float" value="0.05" min="0.0" max="1.0" label="The q-value significance level"/>
50 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe"> 44 <param argument="--fc_corr_p" type="text" label="Name of the Corrected p-value column in the stat dataframe">
51 <validator type="empty_field"/> 45 <validator type="empty_field"/>
52 </param> 46 </param>
53 </when> 47 </when>
54 <when value="false"> 48 <when value="false">
55 <!-- do nothing --> 49 <!-- do nothing -->
56 </when> 50 </when>
57 </conditional> 51 </conditional>
58 <param argument="--feature_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree."/> 52 <param argument="--feature_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the feature dendrogram tree."/>
59 <param argument="--sample_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree."/> 53 <param argument="--sample_cluster_size" value="2" type="integer" label="For tabular output. Number of clusters 'k' to cut the sample dendrogram tree."/>
60 </xml> 54 </xml>
61 <xml name="pca_calcsep"> 55 <xml name="pca_calcsep">
62 <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" 56 <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" label="Calculate separation between groups and include in title?"/>
63 label="Calculate separation between groups and include in title?"/>
64 </xml> 57 </xml>
65 <xml name="target_onto"> 58 <xml name="target_onto">
66 <param argument="--target_onto" type="select" optional="false" 59 <param argument="--target_onto" type="select" optional="false" label="GO category to restrict to">
67 label="GO category to restrict to"> 60 <help>
68 <help>
69 Only the values from this category 61 Only the values from this category
70 of GO terms will be displayed. 62 of GO terms will be displayed.
71 </help> 63 </help>
72 <option value="bp">Biological Process</option> 64 <option value="bp">Biological Process</option>
73 <option value="mf">Molecular Function</option> 65 <option value="mf">Molecular Function</option>
74 <option value="cc">Cellular Component</option> 66 <option value="cc">Cellular Component</option>
75 </param> 67 </param>
76 </xml> 68 </xml>
77 </macros> 69 </macros>
78 <expand macro="requirements" /> 70 <expand macro="xrefs"/>
71 <expand macro="requirements"/>
79 <command detect_errors="exit_code"><![CDATA[ 72 <command detect_errors="exit_code"><![CDATA[
80 #import re 73 #import re
81 #set $safename = re.sub('[^\w\-_\.]', '_', $infile.element_identifier) 74 #set $safename = re.sub('[^\w\-_\.]', '_', $infile.element_identifier)
82 ln -s '$infile' '$safename' 75 ln -s '$infile' '$safename'
83 && 76 &&
170 if test -f 'sample_cluster_${infile.name}.txt'; then mv 'sample_cluster_${infile.name}.txt' sample_cluster_data.txt; fi && 163 if test -f 'sample_cluster_${infile.name}.txt'; then mv 'sample_cluster_${infile.name}.txt' sample_cluster_data.txt; fi &&
171 if test -f 'PC_Data_${infile.name}.txt'; then mv 'PC_Data_${infile.name}.txt' PC_Data.txt; fi 164 if test -f 'PC_Data_${infile.name}.txt'; then mv 'PC_Data_${infile.name}.txt' PC_Data.txt; fi
172 165
173 ]]></command> 166 ]]></command>
174 <inputs> 167 <inputs>
175 <param argument="--infile" type="data" 168 <param argument="--infile" type="data" format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
176 format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/> 169 <expand macro="SAMPS"/>
177 <expand macro="SAMPS"/> 170 <conditional name="mode_args">
178 <conditional name="mode_args"> 171 <param argument="--mode" type="select" label="Mode">
179 <param argument="--mode" type="select" label="Mode"> 172 <option value="f">Functional analysis</option>
180 <option value="f">Functional analysis</option> 173 <option value="t">Taxonomic analysis</option>
181 <option value="t">Taxonomic analysis</option> 174 <option value="ft">Functional-taxonomic interaction analysis</option>
182 <option value="ft">Functional-taxonomic interaction analysis</option> 175 </param>
183 </param> 176 <when value="f">
184 <when value="f"> 177 <param name="ontology" type="select" label="Ontology">
185 <param name="ontology" type="select" label="Ontology"> 178 <option value="go">Gene Ontology (GO terms)</option>
186 <option value="go">Gene Ontology (GO terms)</option> 179 <option value="ec">Enzyme Commission (EC) numbers</option>
187 <option value="ec">Enzyme Commission (EC) numbers</option> 180 <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
188 <option value="cog">Clusters of Orthologous Groups (COG categories)</option> 181 </param>
189 </param> 182 <conditional name="plot">
190 <conditional name="plot"> 183 <param argument="--plottype" type="select" label="Plot type">
191 <param argument="--plottype" type="select" label="Plot type"> 184 <option value="bar">Bar Chart (bar)</option>
192 <option value="bar">Bar Chart (bar)</option> 185 <option value="volcano">Volcano Plot (volcano)</option>
193 <option value="volcano">Volcano Plot (volcano)</option> 186 <option value="heatmap">Heatmap (heatmap)</option>
194 <option value="heatmap">Heatmap (heatmap)</option> 187 <option value="pca">Principal Components Analysis (pca)</option>
195 <option value="pca">Principal Components Analysis (pca)</option> 188 </param>
196 </param> 189 <when value="bar">
197 <when value="bar"> 190 <expand macro="common_bar_params"/>
198 <expand macro="common_bar_params"/> 191 <expand macro="target_onto"/>
199 <expand macro="target_onto"/> 192 <expand macro="barcol"/>
200 <expand macro="barcol"/> 193 </when>
194 <when value="volcano">
195 <expand macro="common_volc_params"/>
196 <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/>
197 </when>
198 <when value="heatmap">
199 <expand macro="common_heatmap_params"/>
200 </when>
201 <when value="pca">
202 <expand macro="pca_calcsep"/>
203 </when>
204 </conditional>
201 </when> 205 </when>
202 <when value="volcano"> 206 <when value="t">
203 <expand macro="common_volc_params"/> 207 <conditional name="plot">
204 <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" 208 <param argument="--plottype" type="select" label="Plot type">
205 label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/> 209 <option value="bar">Bar Chart (bar)</option>
206 </when> 210 <option value="volcano">Volcano Plot (volcano)</option>
207 <when value="heatmap"> 211 <option value="heatmap">Heatmap (heatmap)</option>
208 <expand macro="common_heatmap_params"/> 212 <option value="pca">Principal Components Analysis (pca)</option>
209 </when>
210 <when value="pca">
211 <expand macro="pca_calcsep"/>
212 </when>
213 </conditional>
214 </when>
215 <when value="t">
216 <conditional name="plot">
217 <param argument="--plottype" type="select" label="Plot type">
218 <option value="bar">Bar Chart (bar)</option>
219 <option value="volcano">Volcano Plot (volcano)</option>
220 <option value="heatmap">Heatmap (heatmap)</option>
221 <option value="pca">Principal Components Analysis (pca)</option>
222 </param>
223 <when value="bar">
224 <param argument="--target_rank" type="select"
225 label="Taxonomic rank to restrict to in the plot"
226 help="possibilities are taken from the input dataset.">
227 <options from_dataset="infile">
228 <column name="value" index="2"/>
229 <filter type="unique_value" name="unique_taxon" column="2"/>
230 <!-- <filter type="remove_value" value="rank" column="2"/> -->
231 </options>
232 </param>
233 <expand macro="common_bar_params"/>
234 <expand macro="barcol"/>
235 </when>
236 <when value="volcano">
237 <expand macro="common_volc_params"/>
238 </when>
239 <when value="heatmap">
240 <expand macro="common_heatmap_params"/>
241 </when>
242 <when value="pca">
243 <expand macro="pca_calcsep"/>
244 </when>
245 </conditional>
246 </when>
247 <when value="ft">
248 <conditional name="plot">
249 <param argument="--plottype" type="select" label="Plot type">
250 <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option>
251 </param>
252 <when value="ft_dist">
253 <param argument="--meancol" type="text" label="Mean intensity column name"
254 help="Mean intensity column name for desired experimental condition">
255 <validator type="empty_field"/>
256 </param>
257 <conditional name="margin">
258 <param argument="--whichway" type="select" label="which distribution">
259 <option value="f_dist">functional distribution for a taxon (f_dist)</option>
260 <option value="t_dist">taxonomic distribution for a function (t_dist)</option>
261 </param>
262 <when value="f_dist">
263 <conditional name="term">
264 <param name="id_or_name" type="select" label="">
265 <option value="id" selected="true">Taxon ID</option>
266 <option value="name">Taxon name</option>
267 </param> 213 </param>
268 <when value="id"> 214 <when value="bar">
269 <param argument="--id" type="select" label="Taxon id"> 215 <param argument="--target_rank" type="select" label="Taxonomic rank to restrict to in the plot" help="possibilities are taken from the input dataset.">
270 <options from_dataset="infile"> 216 <options from_dataset="infile">
271 <column name="value" index="3"/> 217 <column name="value" index="2"/>
272 <filter type="unique_value" column="3"/> 218 <filter type="unique_value" name="unique_taxon" column="2"/>
273 <!-- <filter type="remove_value" value="tax_id"/> --> 219 <!-- <filter type="remove_value" value="rank" column="2"/> -->
274 </options> 220 </options>
275 </param> 221 </param>
276 </when> 222 <expand macro="common_bar_params"/>
277 <when value="name"> 223 <expand macro="barcol"/>
278 <param argument="--name" type="select" label="Taxon name"> 224 </when>
279 <options from_dataset="infile"> 225 <when value="volcano">
280 <column name="value" index="4"/> 226 <expand macro="common_volc_params"/>
281 <filter type="unique_value" column="4"/> 227 </when>
282 <!-- <filter type="remove_value" value="taxon_name"/> --> 228 <when value="heatmap">
283 </options> 229 <expand macro="common_heatmap_params"/>
284 </param> 230 </when>
285 </when> 231 <when value="pca">
286 </conditional> 232 <expand macro="pca_calcsep"/>
287 <expand macro="target_onto"/> 233 </when>
288 </when> 234 </conditional>
289 <when value="t_dist"> 235 </when>
290 <conditional name="term"> 236 <when value="ft">
291 <param name="id_or_name" type="select" label=""> 237 <conditional name="plot">
292 <option value="id" selected="true">Functional term ID</option> 238 <param argument="--plottype" type="select" label="Plot type">
293 <option value="name">Functional term name</option> 239 <option value="ft_dist" selected="true">Functional Taxonomic Distribution (ft_dist)</option>
294 </param> 240 </param>
295 <when value="id"> 241 <when value="ft_dist">
296 <param argument="--id" type="select" label="Functional term id"> 242 <param argument="--meancol" type="text" label="Mean intensity column name" help="Mean intensity column name for desired experimental condition">
297 <options from_dataset="infile"> 243 <validator type="empty_field"/>
298 <column name="value" index="0"/>
299 <filter type="unique_value" column="0"/>
300 <!-- <filter type="remove_value" value="go_id"/> -->
301 </options>
302 </param> 244 </param>
303 </when> 245 <conditional name="margin">
304 <when value="name"> 246 <param argument="--whichway" type="select" label="which distribution">
305 <param argument="--name" type="select" label="Functional term name"> 247 <option value="f_dist">functional distribution for a taxon (f_dist)</option>
306 <options from_dataset="infile"> 248 <option value="t_dist">taxonomic distribution for a function (t_dist)</option>
307 <column name="value" index="1"/> 249 </param>
308 <filter type="unique_value" column="1"/> 250 <when value="f_dist">
309 <!-- <filter type="remove_value" value="name"/> --> 251 <conditional name="term">
310 </options> 252 <param name="id_or_name" type="select" label="">
311 </param> 253 <option value="id" selected="true">Taxon ID</option>
312 </when> 254 <option value="name">Taxon name</option>
313 </conditional> 255 </param>
314 <param argument="--target_rank" type="select" 256 <when value="id">
315 label="Taxonomic rank to restrict to in the plot" 257 <param argument="--id" type="select" label="Taxon id">
316 help="possibilities are taken from the input dataset."> 258 <options from_dataset="infile">
317 <options from_dataset="infile"> 259 <column name="value" index="3"/>
318 <column name="value" index="5"/> 260 <filter type="unique_value" column="3"/>
319 <filter type="unique_value" name="unique_taxon" column="5"/> 261 <!-- <filter type="remove_value" value="tax_id"/> -->
320 <!-- <filter type="remove_value" value="rank" column="5"/> --> 262 </options>
321 </options> 263 </param>
322 </param> 264 </when>
323 </when> 265 <when value="name">
324 </conditional> 266 <param argument="--name" type="select" label="Taxon name">
325 <expand macro="barcol"/> 267 <options from_dataset="infile">
268 <column name="value" index="4"/>
269 <filter type="unique_value" column="4"/>
270 <!-- <filter type="remove_value" value="taxon_name"/> -->
271 </options>
272 </param>
273 </when>
274 </conditional>
275 <expand macro="target_onto"/>
276 </when>
277 <when value="t_dist">
278 <conditional name="term">
279 <param name="id_or_name" type="select" label="">
280 <option value="id" selected="true">Functional term ID</option>
281 <option value="name">Functional term name</option>
282 </param>
283 <when value="id">
284 <param argument="--id" type="select" label="Functional term id">
285 <options from_dataset="infile">
286 <column name="value" index="0"/>
287 <filter type="unique_value" column="0"/>
288 <!-- <filter type="remove_value" value="go_id"/> -->
289 </options>
290 </param>
291 </when>
292 <when value="name">
293 <param argument="--name" type="select" label="Functional term name">
294 <options from_dataset="infile">
295 <column name="value" index="1"/>
296 <filter type="unique_value" column="1"/>
297 <!-- <filter type="remove_value" value="name"/> -->
298 </options>
299 </param>
300 </when>
301 </conditional>
302 <param argument="--target_rank" type="select" label="Taxonomic rank to restrict to in the plot" help="possibilities are taken from the input dataset.">
303 <options from_dataset="infile">
304 <column name="value" index="5"/>
305 <filter type="unique_value" name="unique_taxon" column="5"/>
306 <!-- <filter type="remove_value" value="rank" column="5"/> -->
307 </options>
308 </param>
309 </when>
310 </conditional>
311 <expand macro="barcol"/>
312 </when>
313 </conditional>
326 </when> 314 </when>
327 </conditional> 315 </conditional>
328 </when> 316 <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>
329 </conditional> 317 <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>
330 <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>
331 <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>
332 </inputs> 318 </inputs>
333 <outputs> 319 <outputs>
334 <data format="html" name="wrapped_outfile" 320 <data format="html" name="wrapped_outfile" label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html" from_work_dir="wrapped_outfile.html"/>
335 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html" 321 <data format="tabular" name="plotdata" label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data" from_work_dir="plotdata.tab">
336 from_work_dir="wrapped_outfile.html"/> 322 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
337 <data format="tabular" name="plotdata" 323 </data>
338 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data" 324 <data format="tabular" name="heatmap_feature_cluster" label="${mode_args.plot.plottype}: feature cluster data" from_work_dir="feature_cluster_data.txt">
339 from_work_dir="plotdata.tab"> 325 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
340 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter> 326 </data>
341 </data> 327 <data format="tabular" name="heatmap_sample_cluster" label="${mode_args.plot.plottype}: Heatmap sample cluster data" from_work_dir="sample_cluster_data.txt">
342 328 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
343 <data format="tabular" name="heatmap_feature_cluster" 329 </data>
344 label="${mode_args.plot.plottype}: feature cluster data" 330 <data format="tabular" name="pca_sample_cluster" label="${mode_args.plot.plottype}: PCA sample cluster data" from_work_dir="PC_Data.txt">
345 from_work_dir="feature_cluster_data.txt"> 331 <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
346 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter> 332 </data>
347 </data>
348 <data format="tabular" name="heatmap_sample_cluster"
349 label="${mode_args.plot.plottype}: sample cluster data"
350 from_work_dir="sample_cluster_data.txt">
351 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
352 </data>
353
354 <data format="tabular" name="pca_sample_cluster"
355 label="${mode_args.plot.plottype}: sample cluster data"
356 from_work_dir="PC_Data.txt">
357 <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
358 </data>
359
360 </outputs> 333 </outputs>
361 <tests> 334 <tests>
362 <test expect_num_outputs="2"> 335 <test expect_num_outputs="2">
363 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/> 336 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
364 <param name="mode" value="t" /> 337 <param name="mode" value="t"/>
365 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 338 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
366 <param name="plottype" value="bar" /> 339 <param name="plottype" value="bar"/>
367 <param name="target_rank" value="genus" /> 340 <param name="target_rank" value="genus"/>
368 <param name="meancol" value="NS_mean" /> 341 <param name="meancol" value="NS_mean"/>
369 <output name="wrapped_outfile"> 342 <output name="wrapped_outfile">
370 <assert_contents> 343 <assert_contents>
371 <has_text text="To download the image" /> 344 <has_text text="To download the image"/>
372 </assert_contents> 345 </assert_contents>
373 </output> 346 </output>
374 </test> 347 </test>
375 <test expect_num_outputs="2"> 348 <test expect_num_outputs="2">
376 <param name="infile" value="tax_test_out.tab" ftype="tabular"/> 349 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
377 <param name="mode" value="t" /> 350 <param name="mode" value="t"/>
378 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 351 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
379 <param name="plottype" value="volcano" /> 352 <param name="plottype" value="volcano"/>
380 <param name="target_rank" value="genus" /> 353 <param name="target_rank" value="genus"/>
381 <param name="fc_name" value="log2fc_NS_over_WS" /> 354 <param name="fc_name" value="log2fc_NS_over_WS"/>
382 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/> 355 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
383 <param name="textannot" value="taxon_name" /> 356 <param name="textannot" value="taxon_name"/>
384 <output name="wrapped_outfile"> 357 <output name="wrapped_outfile">
385 <assert_contents> 358 <assert_contents>
386 <has_text text="To download the image" /> 359 <has_text text="To download the image"/>
387 </assert_contents> 360 </assert_contents>
388 </output> 361 </output>
389 </test> 362 </test>
390 <test expect_num_outputs="3"> 363 <test expect_num_outputs="3">
391 <param name="infile" value="tax_test_out.tab" ftype="tabular"/> 364 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
392 <param name="mode" value="t" /> 365 <param name="mode" value="t"/>
393 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 366 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
394 <param name="plottype" value="heatmap" /> 367 <param name="plottype" value="heatmap"/>
395 <param name="filter_to_sig" /> 368 <param name="filter_to_sig"/>
396 <param name="alpha" value="0.05" /> 369 <param name="alpha" value="0.05"/>
397 <param name="fc_corr_p" value="corrected_p_NS_over_WS" /> 370 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
398 <param name="feature_cluster_size" value="2" /> 371 <param name="feature_cluster_size" value="2"/>
399 <param name="sample_cluster_size" value="2" /> 372 <param name="sample_cluster_size" value="2"/>
400 <output name="wrapped_outfile"> 373 <output name="wrapped_outfile">
401 <assert_contents> 374 <assert_contents>
402 <has_text text="To download the image" /> 375 <has_text text="To download the image"/>
403 </assert_contents> 376 </assert_contents>
404 </output> 377 </output>
405 <output name="heatmap_feature_cluster"> 378 <output name="heatmap_feature_cluster">
406 <assert_contents> 379 <assert_contents>
407 <has_text text="481" /> 380 <has_text text="481"/>
408 </assert_contents> 381 </assert_contents>
409 </output> 382 </output>
410 </test> 383 </test>
411 <test expect_num_outputs="2"> 384 <test expect_num_outputs="2">
412 <param name="infile" value="tax_test_out.tab" ftype="tabular"/> 385 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
413 <param name="mode" value="t" /> 386 <param name="mode" value="t"/>
414 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 387 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
415 <param name="plottype" value="pca" /> 388 <param name="plottype" value="pca"/>
416 <output name="wrapped_outfile"> 389 <output name="wrapped_outfile">
417 <assert_contents> 390 <assert_contents>
418 <has_text text="To download the image" /> 391 <has_text text="To download the image"/>
419 </assert_contents> 392 </assert_contents>
420 </output> 393 </output>
421 </test> 394 </test>
422 <test expect_num_outputs="2"> 395 <test expect_num_outputs="2">
423 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/> 396 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
424 <param name="mode" value="f" /> 397 <param name="mode" value="f"/>
425 <param name="ontology" value="go" /> 398 <param name="ontology" value="go"/>
426 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 399 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
427 <param name="plottype" value="bar" /> 400 <param name="plottype" value="bar"/>
428 <param name="meancol" value="NS_mean" /> 401 <param name="meancol" value="NS_mean"/>
429 <param name="target_onto" value="bp"/> 402 <param name="target_onto" value="bp"/>
430 <output name="wrapped_outfile"> 403 <output name="wrapped_outfile">
431 <assert_contents> 404 <assert_contents>
432 <has_text text="To download the image" /> 405 <has_text text="To download the image"/>
433 </assert_contents> 406 </assert_contents>
434 </output> 407 </output>
435 </test> 408 </test>
436 <test expect_num_outputs="2"> 409 <test expect_num_outputs="2">
437 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/> 410 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
438 <param name="mode" value="f" /> 411 <param name="mode" value="f"/>
439 <param name="ontology" value="go"/> 412 <param name="ontology" value="go"/>
440 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 413 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
441 <param name="plottype" value="volcano" /> 414 <param name="plottype" value="volcano"/>
442 <param name="fc_name" value="log2fc_NS_over_WS" /> 415 <param name="fc_name" value="log2fc_NS_over_WS"/>
443 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/> 416 <param name="fc_corr_p" value="corrected_p_NS_over_WS"/>
444 <output name="wrapped_outfile"> 417 <output name="wrapped_outfile">
445 <assert_contents> 418 <assert_contents>
446 <has_text text="To download the image" /> 419 <has_text text="To download the image"/>
447 </assert_contents> 420 </assert_contents>
448 </output> 421 </output>
449 </test> 422 </test>
450 <test expect_num_outputs="1"> 423 <test expect_num_outputs="1">
451 <param name="infile" value="tf_filt_out.tab" ftype="tabular"/> 424 <param name="infile" value="tf_filt_out.tab" ftype="tabular"/>
452 <param name="mode" value="ft" /> 425 <param name="mode" value="ft"/>
453 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 426 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
454 <param name="plottype" value="ft_dist" /> 427 <param name="plottype" value="ft_dist"/>
455 <param name="meancol" value="NS_mean" /> 428 <param name="meancol" value="NS_mean"/>
456 <param name="whichway" value="f_dist" /> 429 <param name="whichway" value="f_dist"/>
457 <param name="id_or_name" value="id" /> 430 <param name="id_or_name" value="id"/>
458 <param name="id" value="1301" /> 431 <param name="id" value="1301"/>
459 <param name="target_onto" value="bp" /> 432 <param name="target_onto" value="bp"/>
460 <output name="wrapped_outfile"> 433 <output name="wrapped_outfile">
461 <assert_contents> 434 <assert_contents>
462 <has_text text="To download the image" /> 435 <has_text text="To download the image"/>
463 </assert_contents> 436 </assert_contents>
464 </output> 437 </output>
465 </test> 438 </test>
466 </tests> 439 </tests>
467 <help><![CDATA[ 440 <help><![CDATA[
481 Questions, Comments, Problems, Kudos 454 Questions, Comments, Problems, Kudos
482 -------------------------------------- 455 --------------------------------------
483 456
484 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues. 457 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
485 ]]></help> 458 ]]></help>
486 <expand macro="citations" /> 459 <expand macro="citations"/>
487 </tool> 460 </tool>