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comparison gffread.xml @ 3:9f243677c4c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/gffread commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:41:04 -0500
parents 12aeae6d8587
children 0232f19d300f
comparison
equal deleted inserted replaced
2:12aeae6d8587 3:9f243677c4c6
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>