Mercurial > repos > galaxyp > metaquantome_viz

comparison metaquantome_viz.xml @ 4:1199751329b0 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome commit 7b05dd3aa0714e92d56e4d8c82ee3bcafc8854c2"
author galaxyp
date Sat, 30 Jan 2021 17:57:10 +0000
parents 944b43462104
children 9bf325045235
comparison
equal deleted inserted replaced
3:944b43462104 4:1199751329b0
115 #end if 115 #end if
116 #elif $mode_args.plot.plottype == 'heatmap': 116 #elif $mode_args.plot.plottype == 'heatmap':
117 #if $mode_args.plot.heatmap.filter_to_sig: 117 #if $mode_args.plot.heatmap.filter_to_sig:
118 --filter_to_sig 118 --filter_to_sig
119 --alpha=$mode_args.plot.heatmap.alpha 119 --alpha=$mode_args.plot.heatmap.alpha
120 --fc_corr_p='mode_args.plot.fc_corr_p' 120 --fc_corr_p='$mode_args.plot.heatmap.fc_corr_p'
121 #end if 121 #end if
122 #if $mode_args.plot.feature_cluster_size: 122 #if $mode_args.plot.feature_cluster_size:
123 --feature_cluster_size='$mode_args.plot.feature_cluster_size' 123 --feature_cluster_size='$mode_args.plot.feature_cluster_size'
124 #end if 124 #end if
125 #if $mode_args.plot.sample_cluster_size: 125 #if $mode_args.plot.sample_cluster_size:
163 <p> 163 <p>
164 If text is cut off or the plot is not displaying properly, 164 If text is cut off or the plot is not displaying properly,
165 the easiest fix is to increase the plot dimensions 165 the easiest fix is to increase the plot dimensions
166 </p> 166 </p>
167 </body> 167 </body>
168 </html>" > wrapped_outfile.html 168 </html>" > wrapped_outfile.html &&
169 && >&2 ls 169 if test -f 'feature_cluster_${infile.name}.txt'; then mv 'feature_cluster_${infile.name}.txt' feature_cluster_data.txt; fi &&
170 #if $mode_args.plot.plottype in ["heatmap"] 170 if test -f 'sample_cluster_${infile.name}.txt'; then mv 'sample_cluster_${infile.name}.txt' sample_cluster_data.txt; fi &&
171 && mv 'feature_cluster_${safename}.txt' '$heatmap_feature_cluster' 171 if test -f 'PC_Data_${infile.name}.txt'; then mv 'PC_Data_${infile.name}.txt' PC_Data.txt; fi
172 && mv 'sample_cluster_${safename}.txt' '$heatmap_sample_cluster' 172
173 #end if
174 #if $mode_args.plot.plottype in ["pca"]
175 && mv 'PC_data_${safename}.txt' '$pca_sample_cluster'
176 #end if
177
178 ]]></command> 173 ]]></command>
179 <inputs> 174 <inputs>
180 <param argument="--infile" type="data" 175 <param argument="--infile" type="data"
181 format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/> 176 format="tabular" label="Tabular file from metaQuantome stats or metaQuantome filter" help=""/>
182 <expand macro="SAMPS"/> 177 <expand macro="SAMPS"/>
344 from_work_dir="plotdata.tab"> 339 from_work_dir="plotdata.tab">
345 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter> 340 <filter>mode_args['plot']['plottype'] in ["bar", "volcano"]</filter>
346 </data> 341 </data>
347 342
348 <data format="tabular" name="heatmap_feature_cluster" 343 <data format="tabular" name="heatmap_feature_cluster"
349 label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} feature cluster data"> 344 label="${mode_args.plot.plottype}: feature cluster data"
345 from_work_dir="feature_cluster_data.txt">
350 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter> 346 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
351 </data> 347 </data>
352 <data format="tabular" name="heatmap_sample_cluster" 348 <data format="tabular" name="heatmap_sample_cluster"
353 label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data"> 349 label="${mode_args.plot.plottype}: sample cluster data"
350 from_work_dir="sample_cluster_data.txt">
354 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter> 351 <filter>mode_args['plot']['plottype'] in ["heatmap"]</filter>
355 </data> 352 </data>
356 353
357 <data format="tabular" name="pca_sample_cluster" 354 <data format="tabular" name="pca_sample_cluster"
358 label="${tool.name} on ${on_string}: ${mode_args.plot.plottype} sample cluster data"> 355 label="${mode_args.plot.plottype}: sample cluster data"
356 from_work_dir="PC_Data.txt">
359 <filter>mode_args['plot']['plottype'] in ["pca"]</filter> 357 <filter>mode_args['plot']['plottype'] in ["pca"]</filter>
360 </data> 358 </data>
361 359
362 </outputs> 360 </outputs>
363 <tests> 361 <tests>
388 <has_text text="To download the image" /> 386 <has_text text="To download the image" />
389 </assert_contents> 387 </assert_contents>
390 </output> 388 </output>
391 </test> 389 </test>
392 <test expect_num_outputs="3"> 390 <test expect_num_outputs="3">
393 <param name="infile" value="tax_test_out.tab" ftype="tabular"/> 391 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
394 <param name="mode" value="t" /> 392 <param name="mode" value="t" />
395 <param name="samps" value="rudney_samples.tab" ftype="tabular"/> 393 <param name="samps" value="rudney_samples.tab" ftype="tabular"/>
396 <param name="plottype" value="heatmap" /> 394 <param name="plottype" value="heatmap" />
397 <output name="wrapped_outfile"> 395 <param name="filter_to_sig" />
398 <assert_contents> 396 <param name="alpha" value="0.05" />
399 <has_text text="To download the image" /> 397 <param name="fc_corr_p" value="corrected_p_NS_over_WS" />
400 </assert_contents> 398 <param name="feature_cluster_size" value="2" />
399 <param name="sample_cluster_size" value="2" />
400 <output name="wrapped_outfile">
401 <assert_contents>
402 <has_text text="To download the image" />
403 </assert_contents>
404 </output>
405 <output name="heatmap_feature_cluster">
406 <assert_contents>
407 <has_text text="481" />
408 </assert_contents>
401 </output> 409 </output>
402 </test> 410 </test>
403 <test expect_num_outputs="2"> 411 <test expect_num_outputs="2">
404 <param name="infile" value="tax_test_out.tab" ftype="tabular"/> 412 <param name="infile" value="tax_test_out.tab" ftype="tabular"/>
405 <param name="mode" value="t" /> 413 <param name="mode" value="t" />
407 <param name="plottype" value="pca" /> 415 <param name="plottype" value="pca" />
408 <output name="wrapped_outfile"> 416 <output name="wrapped_outfile">
409 <assert_contents> 417 <assert_contents>
410 <has_text text="To download the image" /> 418 <has_text text="To download the image" />
411 </assert_contents> 419 </assert_contents>
412 </output> 420 </output>
413 </test> 421 </test>
414 <test expect_num_outputs="2"> 422 <test expect_num_outputs="2">
415 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/> 423 <param name="infile" value="func_full_test_out.tab" ftype="tabular"/>
416 <param name="mode" value="f" /> 424 <param name="mode" value="f" />
417 <param name="ontology" value="go" /> 425 <param name="ontology" value="go" />