Mercurial > repos > galaxyp > metaquantome_viz

comparison metaquantome_viz.xml @ 3:944b43462104 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit cf8aec441ba6ef62071c3cf4ac840ebc5a710aa4"
author galaxyp
date Tue, 24 Nov 2020 15:08:30 +0000
parents 02da24eac445
children 1199751329b0
comparison
equal deleted inserted replaced
2:02da24eac445 3:944b43462104
75 </param> 75 </param>
76 </xml> 76 </xml>
77 </macros> 77 </macros>
78 <expand macro="requirements" /> 78 <expand macro="requirements" />
79 <command detect_errors="exit_code"><![CDATA[ 79 <command detect_errors="exit_code"><![CDATA[
80 cp '$infile' '$infile.name' 80 #import re
81 #set $safename = re.sub('[^\w\-_\.]', '_', $infile.element_identifier)
82 ln -s '$infile' '$safename'
81 && 83 &&
82 metaquantome viz 84 metaquantome viz
83 --samps '$samps' 85 --samps '$samps'
84 --mode '$mode_args.mode' 86 --mode '$mode_args.mode'
85 #if str($mode_args.mode) == 'f' 87 #if str($mode_args.mode) == 'f'
86 --ontology='$mode_args.ontology' 88 --ontology='$mode_args.ontology'
87 #end if 89 #end if
88 --infile='$infile.name' 90 --infile='$safename'
89 --plottype='$mode_args.plot.plottype' 91 --plottype='$mode_args.plot.plottype'
90 #if $mode_args.plot.plottype == 'bar': 92 #if $mode_args.plot.plottype == 'bar':
91 #if str($mode_args.mode) == 't': 93 #if str($mode_args.mode) == 't':
92 --target_rank='$mode_args.plot.target_rank' 94 --target_rank='$mode_args.plot.target_rank'
93 #end if 95 #end if
115 #if $mode_args.plot.heatmap.filter_to_sig: 117 #if $mode_args.plot.heatmap.filter_to_sig:
116 --filter_to_sig 118 --filter_to_sig
117 --alpha=$mode_args.plot.heatmap.alpha 119 --alpha=$mode_args.plot.heatmap.alpha
118 --fc_corr_p='mode_args.plot.fc_corr_p' 120 --fc_corr_p='mode_args.plot.fc_corr_p'
119 #end if 121 #end if
120 #if feature_cluster_size: 122 #if $mode_args.plot.feature_cluster_size:
121 --feature_cluster_size='$mode_args.plot.feature_cluster_size' 123 --feature_cluster_size='$mode_args.plot.feature_cluster_size'
122 #end if 124 #end if
123 #if sample_cluster_size: 125 #if $mode_args.plot.sample_cluster_size:
124 --sample_cluster_size='$mode_args.plot.sample_cluster_size' 126 --sample_cluster_size='$mode_args.plot.sample_cluster_size'
125 #end if 127 #end if
126 #elif $mode_args.plot.plottype == 'pca': 128 #elif $mode_args.plot.plottype == 'pca':
127 $mode_args.plot.calculate_sep 129 $mode_args.plot.calculate_sep
128 #elif $mode_args.plot.plottype == 'ft_dist': 130 #elif $mode_args.plot.plottype == 'ft_dist':
162 If text is cut off or the plot is not displaying properly, 164 If text is cut off or the plot is not displaying properly,
163 the easiest fix is to increase the plot dimensions 165 the easiest fix is to increase the plot dimensions
164 </p> 166 </p>
165 </body> 167 </body>
166 </html>" > wrapped_outfile.html 168 </html>" > wrapped_outfile.html
169 && >&2 ls
170 #if $mode_args.plot.plottype in ["heatmap"]
171 && mv 'feature_cluster_${safename}.txt' '$heatmap_feature_cluster'
172 && mv 'sample_cluster_${safename}.txt' '$heatmap_sample_cluster'
173 #end if
174 #if $mode_args.plot.plottype in ["pca"]
175 && mv 'PC_data_${safename}.txt' '$pca_sample_cluster'
176 #end if
177
167 ]]></command> 178 ]]></command>
168 <inputs> 179 <inputs>
169 <param argument="--infile" type="data" 180 <param argument="--infile" type="data"
170 format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/> 181 format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
171 <expand macro="SAMPS"/> 182 <expand macro="SAMPS"/>
327 <outputs> 338 <outputs>
328 <data format="html" name="wrapped_outfile" 339 <data format="html" name="wrapped_outfile"
329 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html" 340 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}.html"
330 from_work_dir="wrapped_outfile.html"/> 341 from_work_dir="wrapped_outfile.html"/>
331 <data format="tabular" name="plotdata" 342 <data format="tabular" name="plotdata"
332 label="${tool.name} ${on_string} ${mode_args.plot.plottype}: plot data" 343 label="${tool.name} on ${on_string} ${mode_args.plot.plottype}: plot data"
333 from_work_dir="plotdata.tab"> 344 from_work_dir="plotdata.tab">
334 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter> 345 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
335 </data> 346 </data>
336 347
337 <data format="tabular" name="heatmap_feature_cluster" 348 <data format="tabular" name="heatmap_feature_cluster"
338 label="${mode_args.plot.plottype}: feature cluster data" 349 label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} feature cluster data">
339 from_work_dir="feature_cluster_${infile.name.rsplit('.',1)[0]}.txt">
340 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter> 350 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
341 </data> 351 </data>
342 <data format="tabular" name="heatmap_sample_cluster" 352 <data format="tabular" name="heatmap_sample_cluster"
343 label="${mode_args.plot.plottype}: sample cluster data" 353 label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
344 from_work_dir="sample_cluster_${infile.name.rsplit('.',1)[0]}.txt">
345 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter> 354 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
346 </data> 355 </data>
347 356
348 <data format="tabular" name="heatmap_sample_cluster" 357 <data format="tabular" name="pca_sample_cluster"
349 label="${mode_args.plot.plottype}: sample cluster data" 358 label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data">
350 from_work_dir="PC_Data_${infile.name.rsplit('.',1)[0]}.txt">
351 <filter>mode_args['plot']['plottype'] in ["pca"]</filter> 359 <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
352 </data> 360 </data>
353 361
354 </outputs> 362 </outputs>
355 <tests> 363 <tests>
356 <test> 364 <test expect_num_outputs="2">
357 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/> 365 <param name="infile" value="tax_filt_out.tab" ftype="tabular"/>
358 <param name="mode" value="t" /> 366 <param name="mode" value="t" />
359 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 367 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
360 <param name="plottype" value="bar" /> 368 <param name="plottype" value="bar" />
361 <param name="target_rank" value="genus" /> 369 <param name="target_rank" value="genus" />
364 <assert_contents> 372 <assert_contents>
365 <has_text text="To download the image" /> 373 <has_text text="To download the image" />
366 </assert_contents> 374 </assert_contents>
367 </output> 375 </output>
368 </test> 376 </test>
369 <test> 377 <test expect_num_outputs="2">
370 <param name="infile" value="tax_test_out.tab" ftype="tabular"/> 378 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
371 <param name="mode" value="t" /> 379 <param name="mode" value="t" />
372 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 380 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
373 <param name="plottype" value="volcano" /> 381 <param name="plottype" value="volcano" />
374 <param name="target_rank" value="genus" /> 382 <param name="target_rank" value="genus" />
379 <assert_contents> 387 <assert_contents>
380 <has_text text="To download the image" /> 388 <has_text text="To download the image" />
381 </assert_contents> 389 </assert_contents>
382 </output> 390 </output>
383 </test> 391 </test>
384 <test> 392 <test expect_num_outputs="3">
385 <param name="infile" value="tax_test_out.tab" ftype="tabular"/> 393 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
386 <param name="mode" value="t" /> 394 <param name="mode" value="t" />
387 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 395 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
388 <param name="plottype" value="heatmap" /> 396 <param name="plottype" value="heatmap" />
389 <output name="wrapped_outfile"> 397 <output name="wrapped_outfile">
390 <assert_contents> 398 <assert_contents>
391 <has_text text="To download the image" /> 399 <has_text text="To download the image" />
392 </assert_contents> 400 </assert_contents>
393 </output> 401 </output>
394 </test> 402 </test>
395 <test> 403 <test expect_num_outputs="2">
396 <param name="infile" value="tax_test_out.tab" ftype="tabular"/> 404 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
397 <param name="mode" value="t" /> 405 <param name="mode" value="t" />
398 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 406 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
399 <param name="plottype" value="pca" /> 407 <param name="plottype" value="pca" />
400 <output name="wrapped_outfile"> 408 <output name="wrapped_outfile">
401 <assert_contents> 409 <assert_contents>
402 <has_text text="To download the image" /> 410 <has_text text="To download the image" />
403 </assert_contents> 411 </assert_contents>
404 </output> 412 </output>
405 </test> 413 </test>
406 <test> 414 <test expect_num_outputs="2">
407 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/> 415 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
408 <param name="mode" value="f" /> 416 <param name="mode" value="f" />
409 <param name="ontology" value="go" /> 417 <param name="ontology" value="go" />
410 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 418 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
411 <param name="plottype" value="bar" /> 419 <param name="plottype" value="bar" />
415 <assert_contents> 423 <assert_contents>
416 <has_text text="To download the image" /> 424 <has_text text="To download the image" />
417 </assert_contents> 425 </assert_contents>
418 </output> 426 </output>
419 </test> 427 </test>
420 <test> 428 <test expect_num_outputs="2">
421 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/> 429 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
422 <param name="mode" value="f" /> 430 <param name="mode" value="f" />
423 <param name="ontology" value="go"/> 431 <param name="ontology" value="go"/>
424 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 432 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
425 <param name="plottype" value="volcano" /> 433 <param name="plottype" value="volcano" />
429 <assert_contents> 437 <assert_contents>
430 <has_text text="To download the image" /> 438 <has_text text="To download the image" />
431 </assert_contents> 439 </assert_contents>
432 </output> 440 </output>
433 </test> 441 </test>
434 <test> 442 <test expect_num_outputs="1">
435 <param name="infile" value="tf_filt_out.tab" ftype="tabular"/> 443 <param name="infile" value="tf_filt_out.tab" ftype="tabular"/>
436 <param name="mode" value="ft" /> 444 <param name="mode" value="ft" />
437 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 445 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
438 <param name="plottype" value="ft_dist" /> 446 <param name="plottype" value="ft_dist" />
439 <param name="meancol" value="NS_mean" /> 447 <param name="meancol" value="NS_mean" />