Mercurial > repos > iuc > homer_findmotifsgenome

comparison homer_findMotifsGenome.xml @ 2:a8f207b43f64 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
author iuc
date Mon, 13 Dec 2021 15:14:25 +0000
parents 3126da33847c
children 4fe92af4542b
comparison
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1:3126da33847c 2:a8f207b43f64
113 $advanced.homer12.neutral 113 $advanced.homer12.neutral
114 -e '$advanced.homer12.e' 114 -e '$advanced.homer12.e'
115 $advanced.homer12.quickMask 115 $advanced.homer12.quickMask
116 -minlp '$advanced.homer12.minlp' 116 -minlp '$advanced.homer12.minlp'
117 #elif str( $advanced.homer12.version ) == "homer1": 117 #elif str( $advanced.homer12.version ) == "homer1":
118 -homer1
118 -depth '$advanced.homer12.depth' 119 -depth '$advanced.homer12.depth'
119 #end if 120 #end if
120 #if str( $background.use ) == "none": 121 #if str( $background.use ) == "none":
121 #if not $nomotif: 122 #if not $nomotif:
122 && cp '${output}'/homerResults.html outputHomer.html 123 && cp '${output}/homerResults.html' outputHomer.html
123 && cp -r '${output}' '${html_homer_file.files_path}' 124 && cp -r '${output}' '${html_homer_file.files_path}'
125 && cp -r '${output}/homerResults' homerResults
124 #end if 126 #end if
125 #if not $motif_options.noknown: 127 #if not $motif_options.noknown:
126 && cp '${output}'/knownResults.html outputKnown.html 128 && cp '${output}/knownResults.html' outputKnown.html
127 && cp -r '${output}' '${html_file.files_path}' 129 && cp -r '${output}' '${html_file.files_path}'
130 && cp -r '${output}/knownResults' knownResults
128 #end if 131 #end if
129 #else 132 #else
130 && cp '${output}'/homerResults.html outputHomer.html 133 && cp '${output}/homerResults.html' outputHomer.html
131 && cp -r '${output}' '${html_homer_file.files_path}' 134 && cp -r '${output}' '${html_homer_file.files_path}'
135 && cp -r '${output}/homerResults' homerResults
132 #end if 136 #end if
133 ]]></command> 137 ]]></command>
134 <inputs> 138 <inputs>
135 <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/> 139 <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/>
136 <conditional name="genome"> 140 <conditional name="genome">
253 <outputs> 257 <outputs>
254 <data format="html" name="html_file" from_work_dir="outputKnown.html" label="${tool.name} on ${on_string}: Known motifs"> 258 <data format="html" name="html_file" from_work_dir="outputKnown.html" label="${tool.name} on ${on_string}: Known motifs">
255 <filter>motif_options['noknown'] is False</filter> 259 <filter>motif_options['noknown'] is False</filter>
256 <filter>background['use'] == "none"</filter> 260 <filter>background['use'] == "none"</filter>
257 </data> 261 </data>
262 <collection name="output_collection_known" type="list" label="${tool.name} on ${on_string}: Known motifs files">
263 <discover_datasets directory="knownResults" pattern="(?P&lt;designation&gt;.+)\.motif" format="txt" visible="false"/>
264 <filter>motif_options['noknown'] is False</filter>
265 <filter>background['use'] == "none"</filter>
266 </collection>
258 <data format="html" name="html_homer_file" from_work_dir="outputHomer.html" label="${tool.name} on ${on_string}: De novo motifs"> 267 <data format="html" name="html_homer_file" from_work_dir="outputHomer.html" label="${tool.name} on ${on_string}: De novo motifs">
259 <filter>nomotif is False</filter> 268 <filter>nomotif is False</filter>
260 </data> 269 </data>
270 <collection name="output_collection_de_novo" type="list" label="${tool.name} on ${on_string}: De novo motifs files">
271 <discover_datasets directory="homerResults" pattern="(?P&lt;designation&gt;.+)\.motif" format="txt" visible="false"/>
272 <filter>nomotif is False</filter>
273 </collection>
261 </outputs> 274 </outputs>
262 <tests> 275 <tests>
276 <test expect_num_outputs="4">
277 <param name="input" value="fake_phix_peaks.bed"/>
278 <conditional name="genome">
279 <param name="source" value="installed"/>
280 <param name="all_fasta_source" value="phiX174"/>
281 </conditional>
282 <output name="html_file" file="motif_test1/knownResults.html" ftype="html" lines_diff="2"/>
283 <output name="html_homer_file">
284 <assert_contents>
285 <has_text text="fake_phix_peaks_bed_motif/ - Homer de novo Motif Results"/>
286 <has_text text="Total target sequences = 1"/>
287 <!-- This is too much impredictible -->
288 <!-- <has_text text="Jaspar"/> -->
289 </assert_contents>
290 </output>
291 <output_collection name="output_collection_known" type="list" count="0">
292 </output_collection>
293 <output_collection name="output_collection_de_novo" type="list">
294 <element name="motif1">
295 <assert_contents>
296 <has_text text=">"/>
297 </assert_contents>
298 </element>
299 </output_collection>
300 </test>
301 <test expect_num_outputs="4">
302 <param name="input" value="CTCF_peaks_shifted.bed"/>
303 <conditional name="genome">
304 <param name="source" value="history"/>
305 <param name="fasta" value="chr2_subset.fa.gz"/>
306 </conditional>
307 <output name="html_file">
308 <assert_contents>
309 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
310 <has_text text="Total Target Sequences = 24"/>
311 <has_text text="CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer"/>
312 </assert_contents>
313 </output>
314 <output name="html_homer_file">
315 <assert_contents>
316 <has_text text="CTCF_peaks_shifted_bed_motif/ - Homer de novo Motif Results"/>
317 <has_text text="Total target sequences = 24"/>
318 <has_text_matching expression="CTCF(Zf)|CTCF/MA|BORIS|CTCFL"/>
319 </assert_contents>
320 </output>
321 <output_collection name="output_collection_known" type="list">
322 <element name="known1">
323 <assert_contents>
324 <has_text text=">"/>
325 </assert_contents>
326 </element>
327 </output_collection>
328 <output_collection name="output_collection_de_novo" type="list">
329 <element name="motif1">
330 <assert_contents>
331 <has_text text=">"/>
332 </assert_contents>
333 </element>
334 </output_collection>
335 </test>
336 <test expect_num_outputs="4">
337 <param name="input" value="CTCF_peaks_shifted.bed"/>
338 <param name="mask" value="true"/>
339 <conditional name="genome">
340 <param name="source" value="history"/>
341 <param name="fasta" value="chr2_subset.fa.gz"/>
342 </conditional>
343 <output name="html_file">
344 <assert_contents>
345 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
346 <has_text text="Total Target Sequences = 18"/>
347 <has_text text="CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer"/>
348 </assert_contents>
349 </output>
350 <output name="html_homer_file">
351 <assert_contents>
352 <has_text text="CTCF_peaks_shifted_bed_motif/ - Homer de novo Motif Results"/>
353 <has_text text="Total target sequences = 18"/>
354 <!-- This is too much impredictible -->
355 <!-- <has_text_matching expression="CTCF(Zf)|CTCF/MA|BORIS|CTCFL|NFATC2"/> -->
356 </assert_contents>
357 </output>
358 <output_collection name="output_collection_known" type="list">
359 <element name="known1">
360 <assert_contents>
361 <has_text text=">"/>
362 </assert_contents>
363 </element>
364 </output_collection>
365 <output_collection name="output_collection_de_novo" type="list">
366 <element name="motif1">
367 <assert_contents>
368 <has_text text=">"/>
369 </assert_contents>
370 </element>
371 </output_collection>
372 </test>
373 <test expect_num_outputs="2">
374 <param name="input" value="CTCF_peaks_shifted.bed"/>
375 <conditional name="genome">
376 <param name="source" value="history"/>
377 <param name="fasta" value="chr2_subset.fa.gz"/>
378 </conditional>
379 <section name="motif_options">
380 <param name="mset" value="plants"/>
381 </section>
382 <param name="nomotif" value="true"/>
383 <output name="html_file">
384 <assert_contents>
385 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
386 <has_text text="Total Target Sequences = 24"/>
387 </assert_contents>
388 </output>
389 <output_collection name="output_collection_known" type="list" count="0">
390 </output_collection>
391 </test>
392 <!-- background tests -->
263 <test expect_num_outputs="2"> 393 <test expect_num_outputs="2">
264 <param name="input" value="fake_phix_peaks.bed"/> 394 <param name="input" value="fake_phix_peaks.bed"/>
265 <conditional name="genome"> 395 <conditional name="genome">
266 <param name="source" value="installed"/> 396 <param name="source" value="installed"/>
267 <param name="all_fasta_source" value="phiX174"/> 397 <param name="all_fasta_source" value="phiX174"/>
268 </conditional> 398 </conditional>
269 <output name="html_file" file="motif_test1/knownResults.html" ftype="html" lines_diff="2"/> 399 <conditional name="background">
400 <param name="use" value="withbg" />
401 <param name="bg" value="fake_phix_peaks.subset.bed" />
402 </conditional>
270 <output name="html_homer_file"> 403 <output name="html_homer_file">
271 <assert_contents> 404 <assert_contents>
272 <has_text text="fake_phix_peaks_bed_motif/ - Homer de novo Motif Results"/> 405 <has_text text="HOXB13/MA0901.2/Jaspar(0.948)"/>
273 <has_text text="Total target sequences = 1"/> 406 <has_text text="Yeast"/>
274 <has_text text="Jaspar"/> 407 </assert_contents>
275 </assert_contents> 408 </output>
276 </output> 409 <output_collection name="output_collection_de_novo" type="list">
410 <element name="motif1">
411 <assert_contents>
412 <has_text text=">"/>
413 </assert_contents>
414 </element>
415 </output_collection>
277 </test> 416 </test>
278 <test expect_num_outputs="2"> 417 <test expect_num_outputs="2">
279 <param name="input" value="CTCF_peaks_shifted.bed"/>
280 <conditional name="genome">
281 <param name="source" value="history"/>
282 <param name="fasta" value="chr2_subset.fa"/>
283 </conditional>
284 <output name="html_file">
285 <assert_contents>
286 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
287 <has_text text="Total Target Sequences = 40"/>
288 <has_text text="CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer"/>
289 </assert_contents>
290 </output>
291 <output name="html_homer_file">
292 <assert_contents>
293 <has_text text="CTCF_peaks_shifted_bed_motif/ - Homer de novo Motif Results"/>
294 <has_text text="Total target sequences = 40"/>
295 <has_text_matching expression="CTCF(Zf)|CTCF/MA|BORIS|CTCFL"/>
296 </assert_contents>
297 </output>
298 </test>
299 <test expect_num_outputs="2">
300 <param name="input" value="CTCF_peaks_shifted.bed"/>
301 <param name="mask" value="true"/>
302 <conditional name="genome">
303 <param name="source" value="history"/>
304 <param name="fasta" value="chr2_subset.fa"/>
305 </conditional>
306 <output name="html_file">
307 <assert_contents>
308 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
309 <has_text text="Total Target Sequences = 34"/>
310 <has_text text="CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer"/>
311 </assert_contents>
312 </output>
313 <output name="html_homer_file">
314 <assert_contents>
315 <has_text text="CTCF_peaks_shifted_bed_motif/ - Homer de novo Motif Results"/>
316 <has_text text="Total target sequences = 34"/>
317 <has_text_matching expression="CTCF(Zf)|CTCF/MA|BORIS|CTCFL"/>
318 </assert_contents>
319 </output>
320 </test>
321 <test expect_num_outputs="1">
322 <param name="input" value="CTCF_peaks_shifted.bed"/>
323 <conditional name="genome">
324 <param name="source" value="history"/>
325 <param name="fasta" value="chr2_subset.fa"/>
326 </conditional>
327 <section name="motif_options">
328 <param name="mset" value="plants"/>
329 </section>
330 <param name="nomotif" value="true"/>
331 <output name="html_file">
332 <assert_contents>
333 <has_text text="CTCF_peaks_shifted_bed_motif - Homer Known Motif Enrichment Results"/>
334 <has_text text="Total Target Sequences = 40"/>
335 <has_text text="RAP26"/>
336 </assert_contents>
337 </output>
338 </test>
339 <!-- background tests -->
340 <test expect_num_outputs="1">
341 <param name="input" value="fake_phix_peaks.bed"/> 418 <param name="input" value="fake_phix_peaks.bed"/>
342 <conditional name="genome"> 419 <conditional name="genome">
343 <param name="source" value="installed"/> 420 <param name="source" value="installed"/>
344 <param name="all_fasta_source" value="phiX174"/> 421 <param name="all_fasta_source" value="phiX174"/>
345 </conditional> 422 </conditional>
346 <conditional name="background"> 423 <conditional name="background">
347 <param name="use" value="withbg" />
348 <param name="bg" value="fake_phix_peaks.subset.bed" />
349 </conditional>
350 <output name="html_homer_file">
351 <assert_contents>
352 <has_text text="HOXB13/MA0901.2/Jaspar(0.948)"/>
353 <has_text text="Yeast"/>
354 </assert_contents>
355 </output>
356 </test>
357 <test expect_num_outputs="1">
358 <param name="input" value="fake_phix_peaks.bed"/>
359 <conditional name="genome">
360 <param name="source" value="installed"/>
361 <param name="all_fasta_source" value="phiX174"/>
362 </conditional>
363 <conditional name="background">
364 <param name="use" value="chopify" /> 424 <param name="use" value="chopify" />
365 <param name="bg" value="fake_phix_peaks.subset.bed" /> 425 <param name="bg" value="fake_phix_peaks.subset.bed" />
366 </conditional> 426 </conditional>
367 <output name="html_homer_file"> 427 <output name="html_homer_file">
368 <assert_contents> 428 <assert_contents>
369 <has_text text="CCA"/> 429 <has_text text="CCA"/>
370 <has_text text="YAP5"/> 430 <has_text text="YAP5"/>
371 </assert_contents> 431 </assert_contents>
372 </output> 432 </output>
433 <output_collection name="output_collection_de_novo" type="list">
434 <element name="motif1">
435 <assert_contents>
436 <has_text text=">"/>
437 </assert_contents>
438 </element>
439 </output_collection>
373 </test> 440 </test>
374 </tests> 441 </tests>
375 <help><![CDATA[ 442 <help><![CDATA[
376 443
377 .. class:: infomark 444 .. class:: infomark