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comparison gffread.xml @ 7:4dea02886337 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 35e5b87300fb4e64d6d4eab376012ca9c524a432"
author iuc
date Mon, 11 Nov 2019 18:27:46 -0500
parents 6ea09f60dee9
children 154d00cbbf2d
comparison
equal deleted inserted replaced
6:6ea09f60dee9 7:4dea02886337
1 <tool id="gffread" name="gffread" version="@VERSION@.1"> 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 <macros> 3 <macros>
4 <token name="@VERSION@">0.11.4</token> 4 <token name="@VERSION@">0.11.6</token>
5 <xml name="fasta_output_select"> 5 <xml name="fasta_output_select">
6 <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">
7 <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>
8 <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x cds.fa)</option> 8 <option value="-x cds.fa">fasta file with spliced CDS for each GFF transcript (-x cds.fa)</option>
9 <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y pep.fa)</option> 9 <option value="-y pep.fa">protein fasta file with the translation of CDS for each record (-y pep.fa)</option>
124 <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters"> 124 <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters">
125 <option value="-U">discard single-exon transcripts (-U)</option> 125 <option value="-U">discard single-exon transcripts (-U)</option>
126 <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option> 126 <option value="-C">coding only: discard mRNAs that have no CDS feature (-C)</option>
127 <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option> 127 <option value="-G">only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input) (-G)</option>
128 <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option> 128 <option value="-O">process also non-transcript GFF records (by default non-transcript records are ignored) (-O)</option>
129 <!-- The no-pseudo option is broken in 0.11.4 of gffread. 129 <option value="--no-pseudo">filter out records matching the 'pseudo' keyword (--no-pseudo)</option>
130 See https://github.com/gpertea/gffread/issues/43 -->
131 <!-- <option value="\-\-no-pseudo">filter out records matching the 'pseudo' keyword (\-\-no-pseudo)</option> -->
132 </param> 130 </param>
133 <conditional name="region"> 131 <conditional name="region">
134 <param name="region_filter" type="select" label="Filter by genome region"> 132 <param name="region_filter" type="select" label="Filter by genome region">
135 <option value="none">No</option> 133 <option value="none">No</option>
136 <option value="filter">Yes</option> 134 <option value="filter">Yes</option>
267 <test> 265 <test>
268 <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"/>
269 <param name="gff_fmt" value="gff"/> 267 <param name="gff_fmt" value="gff"/>
270 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" /> 268 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="2" />
271 </test> 269 </test>
272
273 <test> 270 <test>
274 <param name="input" ftype="gtf" value="ecoli-k12.gff3"/> 271 <param name="input" ftype="gtf" value="ecoli-k12.gff3"/>
275 <param name="gff_fmt" value="gff"/> 272 <param name="gff_fmt" value="gff"/>
276 <param name="full_gff_attribute_preservation" value="-F"/> 273 <param name="full_gff_attribute_preservation" value="-F"/>
277 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" /> 274 <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="2" />
278 </test> 275 </test>
279
280 <!-- The no-pseudo option is broken in 0.11.4 of gffread.
281 See https://github.com/gpertea/gffread/issues/43 -->
282 <!--
283 <test> 276 <test>
284 <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"/>
285 <param name="filtering" value="/-/-no-pseudo"/> # Fix dashes when uncommenting 278 <param name="filtering" value="--no-pseudo"/>
286 <param name="gff_fmt" value="gtf"/> 279 <param name="gff_fmt" value="gtf"/>
287 <output name="output_gtf"> 280 <output name="output_gtf">
288 <assert_contents> 281 <assert_contents>
289 <not_has_text text="pseudo" /> 282 <not_has_text text="pseudo" />
290 </assert_contents> 283 </assert_contents>
291 </output> 284 </output>
292 </test> 285 </test>
293 -->
294
295 <test> 286 <test>
296 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> 287 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
297 <param name="region_filter" value="filter"/> 288 <param name="region_filter" value="filter"/>
298 <param name="range" value="19:496500..504965"/> 289 <param name="range" value="19:496500..504965"/>
299 <param name="gff_fmt" value="gtf"/> 290 <param name="gff_fmt" value="gtf"/>
302 <has_text text="ENST00000587541" /> 293 <has_text text="ENST00000587541" />
303 <has_text text="ENST00000382683" /> 294 <has_text text="ENST00000382683" />
304 </assert_contents> 295 </assert_contents>
305 </output> 296 </output>
306 </test> 297 </test>
307
308 <test> 298 <test>
309 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> 299 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
310 <param name="region_filter" value="filter"/> 300 <param name="region_filter" value="filter"/>
311 <param name="range" value="19:496500..504965"/> 301 <param name="range" value="19:496500..504965"/>
312 <param name="discard_partial" value="true"/> 302 <param name="discard_partial" value="true"/>
316 <not_has_text text="ENST00000587541" /> 306 <not_has_text text="ENST00000587541" />
317 <has_text text="ENST00000382683" /> 307 <has_text text="ENST00000382683" />
318 </assert_contents> 308 </assert_contents>
319 </output> 309 </output>
320 </test> 310 </test>
321
322 <test> 311 <test>
323 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> 312 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
324 <param name="filtering" value="-C"/> 313 <param name="filtering" value="-C"/>
325 <param name="region_filter" value="filter"/> 314 <param name="region_filter" value="filter"/>
326 <param name="range" value="19:496500..504965"/> 315 <param name="range" value="19:496500..504965"/>
330 <not_has_text text="ENST00000587541" /> 319 <not_has_text text="ENST00000587541" />
331 <has_text text="ENST00000382683" /> 320 <has_text text="ENST00000382683" />
332 </assert_contents> 321 </assert_contents>
333 </output> 322 </output>
334 </test> 323 </test>
335
336 <test> 324 <test>
337 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> 325 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
338 <param name="source" value="history"/> 326 <param name="source" value="history"/>
339 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/> 327 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
340 <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/> 328 <param name="fa_outputs" value="-w exons.fa,-x cds.fa,-y pep.fa"/>