Mercurial > repos > devteam > gffread
comparison gffread.xml @ 9:3e436657dcd0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
author | iuc |
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date | Fri, 15 Dec 2023 19:39:24 +0000 |
parents | 154d00cbbf2d |
children |
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8:154d00cbbf2d | 9:3e436657dcd0 |
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1 <tool id="gffread" name="gffread" version="@GALAXY_TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> | 1 <tool id="gffread" name="gffread" version="@GALAXY_TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> |
2 <description>Filters and/or converts GFF3/GTF2 records</description> | 2 <description>Filters and/or converts GFF3/GTF2 records</description> |
3 <xrefs> | |
4 <xref type="bio.tools">gffread</xref> | |
5 </xrefs> | |
6 <macros> | 3 <macros> |
7 <!-- the version of this tool must not be lowered since in the past 2.x was used | 4 <!-- the version of this tool must not be lowered since in the past 2.x was used |
8 lets use small increments and hope that gffread catches up one day --> | 5 lets use small increments and hope that gffread catches up one day --> |
9 <token name="@GALAXY_TOOL_VERSION@">2.2.1.3</token> | 6 <token name="@GALAXY_TOOL_VERSION@">2.2.1.4</token> |
10 <token name="@TOOL_VERSION@">0.12.7</token> | 7 <token name="@TOOL_VERSION@">0.12.7</token> |
11 <token name="@VERSION_SUFFIX@">0</token> | 8 <token name="@VERSION_SUFFIX@">0</token> |
12 <xml name="fasta_output_select"> | 9 <xml name="fasta_output_select"> |
13 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs"> | 10 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs"> |
14 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w)</option> | 11 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w)</option> |
53 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options"> | 50 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options"> |
54 <expand macro="cluster_opts" /> | 51 <expand macro="cluster_opts" /> |
55 </param> | 52 </param> |
56 </xml> | 53 </xml> |
57 </macros> | 54 </macros> |
55 <xrefs> | |
56 <xref type="bio.tools">gffread</xref> | |
57 </xrefs> | |
58 <requirements> | 58 <requirements> |
59 <requirement type="package" version="@TOOL_VERSION@">gffread</requirement> | 59 <requirement type="package" version="@TOOL_VERSION@">gffread</requirement> |
60 </requirements> | 60 </requirements> |
61 <version_command>gffread --version</version_command> | 61 <version_command>gffread --version</version_command> |
62 <command detect_errors="aggressive"> | 62 <command detect_errors="aggressive"> |
114 #if $reference_genome.source != 'none': | 114 #if $reference_genome.source != 'none': |
115 #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '': | 115 #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '': |
116 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(',')) | 116 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(',')) |
117 #end if | 117 #end if |
118 #end if | 118 #end if |
119 | |
119 #if $gffs.gff_fmt != 'none': | 120 #if $gffs.gff_fmt != 'none': |
120 #if $gffs.gff_fmt != 'bed' and $gffs.tname: | 121 #if $gffs.gff_fmt != 'bed' and $gffs.tname: |
121 -t '$gffs.tname' | 122 -t '$gffs.tname' |
122 #end if | 123 #end if |
123 #if $gffs.gff_fmt == 'gff': | 124 #if $gffs.gff_fmt == 'gff': |
124 ## TODO bug 'gft' -> 'gtf' | 125 #if $input.datatype.file_ext == 'gtf': |
125 #if $input.datatype.file_ext == 'gft': | |
126 $gffs.ensembl | 126 $gffs.ensembl |
127 #end if | 127 #end if |
128 #end if | 128 #end if |
129 #if $gffs.gff_fmt == 'gtf' | 129 #if $gffs.gff_fmt == 'gtf' |
130 -T | 130 -T |
131 #elif $gffs.gff_fmt == 'bed' | 131 #elif $gffs.gff_fmt == 'bed' |
132 --bed | 132 --bed |
133 #end if | 133 #end if |
134 -o output.$gffs.gff_fmt | 134 -o output.$gffs.gff_fmt |
135 #else if 'fa_outputs' not in $reference_genome or '.fa' not in str($reference_genome['fa_outputs']) | |
136 -o output.gff | |
135 #end if | 137 #end if |
136 | 138 |
137 ## Missing options | 139 ## Missing options |
138 ## | 140 ## |
139 ## --ids | 141 ## --ids |
251 <!-- reference sequence file --> | 253 <!-- reference sequence file --> |
252 <!-- Error: -g option is required for options -w, -x, -y, -V, -N, -M --> | 254 <!-- Error: -g option is required for options -w, -x, -y, -V, -N, -M --> |
253 <conditional name="reference_genome"> | 255 <conditional name="reference_genome"> |
254 <param name="source" type="select" label="Reference Genome" help="NOTE: Required for fasta outputs"> | 256 <param name="source" type="select" label="Reference Genome" help="NOTE: Required for fasta outputs"> |
255 <option value="none">none</option> | 257 <option value="none">none</option> |
256 <option value="cached"></option> | 258 <option value="cached">Cached reference data</option> |
257 <option value="history">From your history</option> | 259 <option value="history">From your history</option> |
258 </param> | 260 </param> |
259 <when value="none"> | 261 <when value="none"/> |
260 </when> | |
261 <when value="cached"> | 262 <when value="cached"> |
262 <param argument="-g" name="fasta_indexes" type="select" label="Source FASTA Sequence"> | 263 <param argument="-g" name="fasta_indexes" type="select" label="Source FASTA Sequence"> |
263 <options from_data_table="all_fasta"/> | 264 <options from_data_table="all_fasta"/> |
264 </param> | 265 </param> |
265 <expand macro="ref_filtering_select" /> | 266 <expand macro="ref_filtering_select" /> |
278 <option value="none">none</option> | 279 <option value="none">none</option> |
279 <option value="gff">GFF</option> | 280 <option value="gff">GFF</option> |
280 <option value="gtf">GTF</option> | 281 <option value="gtf">GTF</option> |
281 <option value="bed">BED</option> | 282 <option value="bed">BED</option> |
282 </param> | 283 </param> |
283 <when value="none"> | 284 <when value="none"/> |
284 </when> | |
285 <when value="gff"> | 285 <when value="gff"> |
286 <param argument="-L" name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help=""/> | 286 <param argument="-L" name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help=""/> |
287 <expand macro="trackname" /> | 287 <expand macro="trackname" /> |
288 </when> | 288 </when> |
289 <when value="gtf"> | 289 <when value="gtf"> |
290 <expand macro="trackname" /> | 290 <expand macro="trackname" /> |
291 </when> | 291 </when> |
292 <when value="bed"> | 292 <when value="bed"/> |
293 </when> | |
294 </conditional> | 293 </conditional> |
295 | 294 |
296 <param argument="-F" name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false" | 295 <param argument="-F" name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false" |
297 label="full GFF attribute preservation (all attributes are shown)" help=""/> | 296 label="full GFF attribute preservation (all attributes are shown)" help=""/> |
298 <param argument="-D" name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false" | 297 <param argument="-D" name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false" |
301 label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help=""/> | 300 label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help=""/> |
302 | 301 |
303 </inputs> | 302 </inputs> |
304 <outputs> | 303 <outputs> |
305 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff"> | 304 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff"> |
306 <filter>gffs['gff_fmt'] == 'gff'</filter> | 305 <!-- output gff also if the user deselected all outputs: none is selected and all .fa outputs are disabled --> |
306 <filter>gffs['gff_fmt'] == 'gff' or (gffs['gff_fmt'] == 'none' and ('fa_outputs' not in reference_genome or '.fa' not in str(reference_genome['fa_outputs'])))</filter> | |
307 </data> | 307 </data> |
308 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf"> | 308 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf"> |
309 <filter>gffs['gff_fmt'] == 'gtf'</filter> | 309 <filter>gffs['gff_fmt'] == 'gtf'</filter> |
310 </data> | 310 </data> |
311 <data name="output_bed" format="bed" metadata_source="input" label="${tool.name} on ${on_string}: bed" from_work_dir="output.bed"> | 311 <data name="output_bed" format="bed" metadata_source="input" label="${tool.name} on ${on_string}: bed" from_work_dir="output.bed"> |
327 <tests> | 327 <tests> |
328 <test expect_num_outputs="1"> | 328 <test expect_num_outputs="1"> |
329 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 329 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
330 <param name="gff_fmt" value="gff"/> | 330 <param name="gff_fmt" value="gff"/> |
331 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" /> | 331 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" /> |
332 <assert_stdout> | |
333 <has_n_lines n="0"/> | |
334 </assert_stdout> | |
335 </test> | |
336 <!-- mapping --> | |
337 <test expect_num_outputs="1"> | |
338 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | |
339 <param name="gff_fmt" value="gff"/> | |
340 <param name="chr_replace" ftype="tabular" value="chr_replace"/> | |
341 <output name="output_gff" ftype="gff3"> | |
342 <assert_contents> | |
343 <has_n_lines n="314"/> | |
344 <has_line_matching expression="^chr.*"/> | |
345 <has_line_matching expression="^1.*" negate="true"/> | |
346 </assert_contents> | |
347 </output> | |
348 <assert_stdout> | |
349 <has_n_lines n="0"/> | |
350 </assert_stdout> | |
351 </test> | |
352 <!-- none output and all .fa outputs deselected .. gff is produced anyway, since we need one output --> | |
353 <test expect_num_outputs="1"> | |
354 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | |
355 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" /> | |
356 <assert_stdout> | |
357 <has_n_lines n="0"/> | |
358 </assert_stdout> | |
359 </test> | |
360 <!-- test ensemble gtf to gff conversion --> | |
361 <test expect_num_outputs="1"> | |
362 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | |
363 <conditional name="gffs"> | |
364 <param name="gff_fmt" value="gff"/> | |
365 <param name="ensembl" value="true"/> | |
366 <param name="tname" value="track name"/> | |
367 </conditional> | |
368 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71_ensemble.gff3" ftype="gff3" lines_diff="4" /> | |
369 <assert_command> | |
370 <has_text text="-L"/> | |
371 <has_text text="-t 'track name'"/> | |
372 </assert_command> | |
373 <assert_stdout> | |
374 <has_n_lines n="0"/> | |
375 </assert_stdout> | |
332 </test> | 376 </test> |
333 <test expect_num_outputs="1"> | 377 <test expect_num_outputs="1"> |
334 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 378 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
335 <param name="gff_fmt" value="gff"/> | 379 <param name="gff_fmt" value="gff"/> |
336 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" /> | 380 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" /> |
381 <assert_stdout> | |
382 <has_n_lines n="0"/> | |
383 </assert_stdout> | |
337 </test> | 384 </test> |
338 <test expect_num_outputs="1"> | 385 <test expect_num_outputs="1"> |
339 <param name="input" ftype="gtf" value="ecoli-k12.gff3"/> | 386 <param name="input" ftype="gtf" value="ecoli-k12.gff3"/> |
340 <param name="gff_fmt" value="gff"/> | 387 <param name="gff_fmt" value="gff"/> |
341 <param name="full_gff_attribute_preservation" value="-F"/> | 388 <param name="full_gff_attribute_preservation" value="-F"/> |
342 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="4" /> | 389 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="4" /> |
390 <assert_stdout> | |
391 <has_n_lines n="0"/> | |
392 </assert_stdout> | |
343 </test> | 393 </test> |
344 <!-- bed output --> | 394 <!-- bed output --> |
345 <test expect_num_outputs="1"> | 395 <test expect_num_outputs="1"> |
346 <param name="input" ftype="gff3" value="Homo_sapiens.GRCh37_19.71.gff3"/> | 396 <param name="input" ftype="gff3" value="Homo_sapiens.GRCh37_19.71.gff3"/> |
347 <param name="gff_fmt" value="bed"/> | 397 <param name="gff_fmt" value="bed"/> |
349 <assert_contents> | 399 <assert_contents> |
350 <has_n_lines n="42"/> | 400 <has_n_lines n="42"/> |
351 <has_n_columns n="13"/> | 401 <has_n_columns n="13"/> |
352 </assert_contents> | 402 </assert_contents> |
353 </output> | 403 </output> |
404 <assert_stdout> | |
405 <has_n_lines n="0"/> | |
406 </assert_stdout> | |
354 </test> | 407 </test> |
355 <!-- bed input and test tname --> | 408 <!-- bed input and test tname --> |
356 <test expect_num_outputs="1"> | 409 <test expect_num_outputs="1"> |
357 <param name="input" ftype="bed" value="Homo_sapiens.GRCh37_19.71.bed"/> | 410 <param name="input" ftype="bed" value="Homo_sapiens.GRCh37_19.71.bed"/> |
358 <param name="gff_fmt" value="gff"/> | 411 <param name="gff_fmt" value="gff"/> |
363 <!-- this will work with https://github.com/galaxyproject/galaxy/pull/12528 --> | 416 <!-- this will work with https://github.com/galaxyproject/galaxy/pull/12528 --> |
364 <!-- <has_n_columns n="9" comment="#"/> --> | 417 <!-- <has_n_columns n="9" comment="#"/> --> |
365 <has_text text="track name"/> | 418 <has_text text="track name"/> |
366 </assert_contents> | 419 </assert_contents> |
367 </output> | 420 </output> |
421 <assert_stdout> | |
422 <has_n_lines n="0"/> | |
423 </assert_stdout> | |
368 </test> | 424 </test> |
369 <test expect_num_outputs="1"> | 425 <test expect_num_outputs="1"> |
370 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 426 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
371 <param name="region_filter" value="filter"/> | 427 <param name="region_filter" value="filter"/> |
372 <param name="range" value="19:496500..504965"/> | 428 <param name="range" value="19:496500..504965"/> |
375 <assert_contents> | 431 <assert_contents> |
376 <has_text text="ENST00000587541" /> | 432 <has_text text="ENST00000587541" /> |
377 <has_text text="ENST00000382683" /> | 433 <has_text text="ENST00000382683" /> |
378 </assert_contents> | 434 </assert_contents> |
379 </output> | 435 </output> |
436 <assert_stdout> | |
437 <has_n_lines n="0"/> | |
438 </assert_stdout> | |
380 </test> | 439 </test> |
381 <test expect_num_outputs="1"> | 440 <test expect_num_outputs="1"> |
382 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 441 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
383 <param name="region_filter" value="filter"/> | 442 <param name="region_filter" value="filter"/> |
384 <param name="range" value="19:496500..504965"/> | 443 <param name="range" value="19:496500..504965"/> |
388 <assert_contents> | 447 <assert_contents> |
389 <not_has_text text="ENST00000587541" /> | 448 <not_has_text text="ENST00000587541" /> |
390 <has_text text="ENST00000382683" /> | 449 <has_text text="ENST00000382683" /> |
391 </assert_contents> | 450 </assert_contents> |
392 </output> | 451 </output> |
452 <assert_stdout> | |
453 <has_n_lines n="0"/> | |
454 </assert_stdout> | |
393 </test> | 455 </test> |
394 <test expect_num_outputs="1"> | 456 <test expect_num_outputs="1"> |
395 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 457 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
396 <param name="filtering" value="-C"/> | 458 <param name="filtering" value="-C"/> |
397 <param name="region_filter" value="filter"/> | 459 <param name="region_filter" value="filter"/> |
401 <assert_contents> | 463 <assert_contents> |
402 <not_has_text text="ENST00000587541" /> | 464 <not_has_text text="ENST00000587541" /> |
403 <has_text text="ENST00000382683" /> | 465 <has_text text="ENST00000382683" /> |
404 </assert_contents> | 466 </assert_contents> |
405 </output> | 467 </output> |
468 <assert_stdout> | |
469 <has_n_lines n="0"/> | |
470 </assert_stdout> | |
406 </test> | 471 </test> |
407 <test expect_num_outputs="4"> | 472 <test expect_num_outputs="4"> |
408 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 473 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
409 <param name="source" value="history"/> | 474 <param name="source" value="history"/> |
410 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/> | 475 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/> |
434 <assert_contents> | 499 <assert_contents> |
435 <has_text text="ENST00000346144" /> | 500 <has_text text="ENST00000346144" /> |
436 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" /> | 501 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" /> |
437 </assert_contents> | 502 </assert_contents> |
438 </output> | 503 </output> |
504 <assert_stdout> | |
505 <has_n_lines n="0"/> | |
506 </assert_stdout> | |
439 </test> | 507 </test> |
440 <test expect_num_outputs="1"> | 508 <test expect_num_outputs="1"> |
441 <param name="input" ftype="gtf" value="stop_codons.gtf"/> | 509 <param name="input" ftype="gtf" value="stop_codons.gtf"/> |
442 <param name="source" value="history"/> | 510 <param name="source" value="history"/> |
443 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/> | 511 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/> |
446 <assert_contents> | 514 <assert_contents> |
447 <has_text text="ENST00000269812" /> | 515 <has_text text="ENST00000269812" /> |
448 <has_text text="PLRGLHPRV*LQTPLERCPCWPPAGGTGGCPHCLLHLRLLQSPTPTALSEGGGAGTEAQPVTDVDPGRG*" /> | 516 <has_text text="PLRGLHPRV*LQTPLERCPCWPPAGGTGGCPHCLLHLRLLQSPTPTALSEGGGAGTEAQPVTDVDPGRG*" /> |
449 </assert_contents> | 517 </assert_contents> |
450 </output> | 518 </output> |
519 <assert_stdout> | |
520 <has_n_lines n="0"/> | |
521 </assert_stdout> | |
451 </test> | 522 </test> |
452 </tests> | 523 </tests> |
453 <help> | 524 <help> |
454 <![CDATA[ | 525 <![CDATA[ |
455 **gffread Filters and/or converts GFF3/GTF2 records** | 526 **gffread Filters and/or converts GFF3/GTF2 records** |