Mercurial > repos > devteam > gffread
comparison gffread.xml @ 3:9f243677c4c6 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author | devteam |
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date | Tue, 07 Feb 2017 18:41:04 -0500 |
parents | 12aeae6d8587 |
children | 0232f19d300f |
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2:12aeae6d8587 | 3:9f243677c4c6 |
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1 <tool id="gffread" name="gffread" version="@VERSION@.0"> | 1 <tool id="gffread" name="gffread" version="@VERSION@.0"> |
2 <description>Filters and/or converts GFF3/GTF2 records</description> | 2 <description>Filters and/or converts GFF3/GTF2 records</description> |
3 <expand macro="requirements" /> | |
4 <expand macro="stdio" /> | |
5 <macros> | 3 <macros> |
6 <import>cuff_macros.xml</import> | 4 <import>cuff_macros.xml</import> |
7 <xml name="fasta_output_select"> | 5 <xml name="fasta_output_select"> |
8 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs"> | 6 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs"> |
9 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option> | 7 <option value="-w exons.fa">fasta file with spliced exons for each GFF transcript (-w exons.fa)</option> |
47 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options"> | 45 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options"> |
48 <expand macro="cluster_opts" /> | 46 <expand macro="cluster_opts" /> |
49 </param> | 47 </param> |
50 </xml> | 48 </xml> |
51 </macros> | 49 </macros> |
50 <expand macro="requirements" /> | |
51 <expand macro="stdio" /> | |
52 <command> | 52 <command> |
53 <![CDATA[ | 53 <![CDATA[ |
54 #if $reference_genome.source == 'history': | 54 #if $reference_genome.source == 'history': |
55 ln -s $reference_genome.genome_fasta genomeref.fa && | 55 ln -s '$reference_genome.genome_fasta' genomeref.fa && |
56 #end if | 56 #end if |
57 gffread $input | 57 gffread '$input' |
58 #if $reference_genome.source == 'cached': | 58 #if $reference_genome.source == 'cached': |
59 -g "${reference_genome.fasta_indexes.fields.path}" | 59 -g '${reference_genome.fasta_indexes.fields.path}' |
60 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '': | 60 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '': |
61 #echo ' '.join(str($reference_genome.ref_filtering).split(',')) | 61 #echo ' '.join(str($reference_genome.ref_filtering).split(',')) |
62 #end if | 62 #end if |
63 #elif $reference_genome.source == 'history': | 63 #elif $reference_genome.source == 'history': |
64 -g genomeref.fa | 64 -g genomeref.fa |
72 #end if | 72 #end if |
73 #if $maxintron and $maxintron > 0: | 73 #if $maxintron and $maxintron > 0: |
74 -i $maxintron | 74 -i $maxintron |
75 #end if | 75 #end if |
76 #if $region.region_filter == 'filter': | 76 #if $region.region_filter == 'filter': |
77 -r $region.range $region.discard_partial | 77 -r '$region.range' $region.discard_partial |
78 #end if | 78 #end if |
79 #if $merging.merge_sel != 'none': | 79 #if $merging.merge_sel != 'none': |
80 $merging.merge_cmd | 80 $merging.merge_cmd |
81 #if $merging.merge_options: | 81 #if $merging.merge_options: |
82 #echo ' '.join(str($merging.merge_options).split(',')) | 82 #echo ' '.join(str($merging.merge_options).split(',')) |
83 #end if | 83 #end if |
84 #end if | 84 #end if |
85 #if $chr_replace: | 85 #if $chr_replace: |
86 -m "$chr_replace" | 86 -m '$chr_replace' |
87 #end if | 87 #end if |
88 ## | 88 ## |
89 ## Although documented, does not appear to be used in the gffread code | 89 ## Although documented, does not appear to be used in the gffread code |
90 ## #if $seq_info: | 90 ## #if $seq_info: |
91 ## -A -s "$seq_info" | 91 ## -A -s "$seq_info" |
97 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(',')) | 97 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(',')) |
98 #end if | 98 #end if |
99 #end if | 99 #end if |
100 #if $gffs.gff_fmt != 'none': | 100 #if $gffs.gff_fmt != 'none': |
101 #if $gffs.tname: | 101 #if $gffs.tname: |
102 -t "$gffs.tname" | 102 -t '$gffs.tname' |
103 #end if | 103 #end if |
104 #if $gffs.gff_fmt == 'gff': | 104 #if $gffs.gff_fmt == 'gff': |
105 #if $input.datatype.file_ext == 'gft': | 105 #if $input.datatype.file_ext == 'gft': |
106 $gffs.ensembl | 106 $gffs.ensembl |
107 #end if | 107 #end if |
139 -chr1:1000..500000 | 139 -chr1:1000..500000 |
140 ]]> | 140 ]]> |
141 </help> | 141 </help> |
142 <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator> | 142 <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator> |
143 </param> | 143 </param> |
144 <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" check="false" | 144 <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" checked="false" |
145 label="discard all transcripts that are not fully contained within the given range" help="(-R)"/> | 145 label="Discard all transcripts that are not fully contained within the given range" help="(-R)"/> |
146 </when> | 146 </when> |
147 </conditional> | 147 </conditional> |
148 <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns" | 148 <param name="maxintron" type="integer" value="" optional="true" min="0" label="Filter out transcipts with large introns" |
149 help="If set, discard transcripts having an intron larger (-i max_intron)"/> | 149 help="If set, discard transcripts having an intron larger (-i max_intron)"/> |
150 <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" > | 150 <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names" > |
216 </param> | 216 </param> |
217 <when value="none"> | 217 <when value="none"> |
218 </when> | 218 </when> |
219 <when value="gff"> | 219 <when value="gff"> |
220 <param name="output_cmd" type="hidden" value="-o output.gff3"/> | 220 <param name="output_cmd" type="hidden" value="-o output.gff3"/> |
221 <param name="ensembl" type="boolean" truevalue="-L" falsevalue="" check="false" label="Ensembl GTF to GFF3 conversion" help="(-L)"/> | 221 <param name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help="(-L)"/> |
222 <expand macro="trackname" /> | 222 <expand macro="trackname" /> |
223 </when> | 223 </when> |
224 <when value="gtf"> | 224 <when value="gtf"> |
225 <param name="output_cmd" type="hidden" value="-T -o output.gtf"/> | 225 <param name="output_cmd" type="hidden" value="-T -o output.gtf"/> |
226 <expand macro="trackname" /> | 226 <expand macro="trackname" /> |
227 </when> | 227 </when> |
228 </conditional> | 228 </conditional> |
229 | 229 |
230 <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" check="false" | 230 <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false" |
231 label="full GFF attribute preservation (all attributes are shown)" help="(-F)"/> | 231 label="full GFF attribute preservation (all attributes are shown)" help="(-F)"/> |
232 <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" check="false" | 232 <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" checked="false" |
233 label="decode url encoded characters within attributes" help="(-D)"/> | 233 label="decode url encoded characters within attributes" help="(-D)"/> |
234 <param name="expose" type="boolean" truevalue="-E" falsevalue="" check="false" | 234 <param name="expose" type="boolean" truevalue="-E" falsevalue="" checked="false" |
235 label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help="(-E)"/> | 235 label="warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records" help="(-E)"/> |
236 | 236 |
237 </inputs> | 237 </inputs> |
238 <outputs> | 238 <outputs> |
239 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff3"> | 239 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff3"> |
257 </outputs> | 257 </outputs> |
258 <tests> | 258 <tests> |
259 <test> | 259 <test> |
260 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 260 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
261 <param name="gff_fmt" value="gff"/> | 261 <param name="gff_fmt" value="gff"/> |
262 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" /> | 262 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" /> |
263 </test> | 263 </test> |
264 | 264 |
265 <test> | 265 <test> |
266 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 266 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
267 <param name="filtering" value="--no-pseudo"/> | 267 <param name="filtering" value="--no-pseudo"/> |
268 <param name="gff_fmt" value="gtf"/> | 268 <param name="gff_fmt" value="gtf"/> |
269 <output name="output_gtf"> | 269 <output name="output_gtf"> |
270 <assert_contents> | 270 <assert_contents> |
271 <not_has_text text="pseudo" /> | 271 <not_has_text text="pseudo" /> |
272 </assert_contents> | 272 </assert_contents> |
273 </output> | 273 </output> |
274 </test> | 274 </test> |
275 | 275 |
276 <test> | 276 <test> |
277 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 277 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
280 <param name="gff_fmt" value="gtf"/> | 280 <param name="gff_fmt" value="gtf"/> |
281 <output name="output_gtf"> | 281 <output name="output_gtf"> |
282 <assert_contents> | 282 <assert_contents> |
283 <has_text text="ENST00000587541" /> | 283 <has_text text="ENST00000587541" /> |
284 <has_text text="ENST00000382683" /> | 284 <has_text text="ENST00000382683" /> |
285 </assert_contents> | 285 </assert_contents> |
286 </output> | 286 </output> |
287 </test> | 287 </test> |
288 | 288 |
289 <test> | 289 <test> |
290 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 290 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
292 <param name="range" value="19:496500..504965"/> | 292 <param name="range" value="19:496500..504965"/> |
293 <param name="discard_partial" value="true"/> | 293 <param name="discard_partial" value="true"/> |
294 <param name="gff_fmt" value="gtf"/> | 294 <param name="gff_fmt" value="gtf"/> |
295 <output name="output_gtf"> | 295 <output name="output_gtf"> |
296 <assert_contents> | 296 <assert_contents> |
297 <has_text text="ENST00000587541" /> | 297 <not_has_text text="ENST00000587541" /> |
298 <has_text text="ENST00000382683" /> | 298 <has_text text="ENST00000382683" /> |
299 </assert_contents> | 299 </assert_contents> |
300 </output> | 300 </output> |
301 </test> | 301 </test> |
302 | 302 |
303 <test> | 303 <test> |
304 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 304 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
308 <param name="gff_fmt" value="gtf"/> | 308 <param name="gff_fmt" value="gtf"/> |
309 <output name="output_gtf"> | 309 <output name="output_gtf"> |
310 <assert_contents> | 310 <assert_contents> |
311 <not_has_text text="ENST00000587541" /> | 311 <not_has_text text="ENST00000587541" /> |
312 <has_text text="ENST00000382683" /> | 312 <has_text text="ENST00000382683" /> |
313 </assert_contents> | 313 </assert_contents> |
314 </output> | 314 </output> |
315 </test> | 315 </test> |
316 | 316 |
317 <test> | 317 <test> |
318 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> | 318 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> |
319 <param name="source" value="history"/> | 319 <param name="source" value="history"/> |
320 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/> | 320 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/> |
321 <param name="fa_outputs" value="-w exons.f,-x cds.fa,-y pep.fa"/> | 321 <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/> |
322 <param name="region_filter" value="filter"/> | 322 <param name="region_filter" value="filter"/> |
323 <param name="range" value="19:496500..504965"/> | 323 <param name="range" value="19:496500..504965"/> |
324 <param name="gff_fmt" value="gtf"/> | 324 <param name="gff_fmt" value="gtf"/> |
325 <output name="output_gtf"> | 325 <output name="output_gtf"> |
326 <assert_contents> | 326 <assert_contents> |
327 <not_has_text text="ENST00000587541" /> | 327 <not_has_text text="ENST00000587541" /> |
328 <has_text text="ENST00000382683" /> | 328 <has_text text="ENST00000382683" /> |
329 </assert_contents> | 329 </assert_contents> |
330 </output> | 330 </output> |
331 <output name="output_exons"> | 331 <output name="output_exons"> |
332 <assert_contents> | 332 <assert_contents> |
333 <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" /> | 333 <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" /> |
334 <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" /> | 334 <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" /> |
335 </assert_contents> | 335 </assert_contents> |
336 </output> | 336 </output> |
337 <output name="output_cds"> | 337 <output name="output_cds"> |
338 <assert_contents> | 338 <assert_contents> |
339 <has_text text="ENST00000346144 gene=MADCAM1" /> | 339 <has_text text="ENST00000346144 gene=MADCAM1" /> |
340 <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" /> | 340 <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" /> |
341 </assert_contents> | 341 </assert_contents> |
342 </output> | 342 </output> |
343 <output name="output_pep"> | 343 <output name="output_pep"> |
344 <assert_contents> | 344 <assert_contents> |
345 <has_text text="ENST00000346144 gene=MADCAM1" /> | 345 <has_text text="ENST00000346144 gene=MADCAM1" /> |
346 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" /> | 346 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" /> |
347 </assert_contents> | 347 </assert_contents> |
348 </output> | 348 </output> |
349 </test> | 349 </test> |
350 | 350 |
351 </tests> | 351 </tests> |
352 <help> | 352 <help> |