|
0
|
1 <tool id="gffread" name="gffread" version="2.2.1">
|
|
|
2 <description>Filters and/or converts GFF3/GTF2 records</description>
|
|
|
3 <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description>
|
|
|
4 <expand macro="requirements" />
|
|
|
5 <expand macro="stdio" />
|
|
|
6 <macros>
|
|
|
7 <import>cuff_macros.xml</import>
|
|
|
8 <xml name="fasta_output_select">
|
|
|
9 <param name="fa_outputs" type="select" display="checkboxes" multiple="true" label="Select fasta outputs">
|
|
|
10 <option value="-w exons.fa">(-w) a fasta file with spliced exons for each GFF transcript</option>
|
|
|
11 <option value="-x cds.fa">(-x) a fasta file with spliced CDS for each GFF transcript</option>
|
|
|
12 <option value="-y pep.fa">(-y) a protein fasta file with the translation of CDS for each record</option>
|
|
|
13 <option value="-W">(-W) for each fasta record the exon coordinates projected onto the spliced sequence</option>
|
|
|
14 </param>
|
|
|
15 </xml>
|
|
|
16 <xml name="ref_filtering_select">
|
|
|
17 <param name="ref_filtering" type="select" display="checkboxes" multiple="true" label="reference based filters">
|
|
|
18 <option value="-N">(-N) discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)</option>
|
|
|
19 <option value="-J">(-J) discard any mRNAs that either lack initial START codon or the terminal STOP codon, or have an in-frame stop codon (only print mRNAs with a fulll, valid CDS)</option>
|
|
|
20 <option value="-V">(-V) discard any mRNAs with CDS having in-frame stop codons</option>
|
|
|
21 <option value="-H">(-H with -V) check and adjust the starting CDS phase if the original phase leads to a translation with an in-frame stop codon</option>
|
|
|
22 <option value="-B">(-B with -V) single-exon transcripts are also checked on the opposite strand</option>
|
|
|
23 </param>
|
|
|
24 </xml>
|
|
|
25 <xml name="trackname">
|
|
|
26 <param name="tname" type="text" value="" optional="true" label="(-t) Trackname to use in the second column of each GFF output line">
|
|
|
27 <validator type="regex">\w+</validator>
|
|
|
28 </param>
|
|
|
29 </xml>
|
|
|
30 <xml name="merge_opts">
|
|
|
31 <option value="-K">(-K) also collapse shorter, fully contained transcripts with fewer introns than the container</option>
|
|
|
32 <option value="-Q">(-Q) remove the containment restriction (multi-exon transcripts will be collapsed if just their introns match, while single-exon transcripts can partially overlap 80%)</option>
|
|
|
33 <option value="-d dupinfo">(-d) output collapsing info</option>
|
|
|
34 </xml>
|
|
|
35 <xml name="cluster_opts">
|
|
|
36 <option value="--force-exons">(--force-exons) make sure that the lowest level GFF features are printed as 'exon' features</option>
|
|
|
37 <option value="-Z">(-Z) merge close exons into a single exon (for intron size < 4)</option>
|
|
|
38 </xml>
|
|
|
39 <xml name="merge_opt_sel">
|
|
|
40 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Merge options">
|
|
|
41 <expand macro="cluster_opts" />
|
|
|
42 <expand macro="merge_opts" />
|
|
|
43 </param>
|
|
|
44 </xml>
|
|
|
45 <xml name="cluster_opt_sel">
|
|
|
46 <param name="merge_options" type="select" display="checkboxes" multiple="true" label="Cluster options">
|
|
|
47 <expand macro="cluster_opts" />
|
|
|
48 </param>
|
|
|
49 </xml>
|
|
|
50 </macros>
|
|
|
51 <command>
|
|
|
52 <![CDATA[
|
|
|
53 #if $reference_genome.source == 'history':
|
|
|
54 ln -s $reference_genome.genome_fasta genomeref.fa &&
|
|
|
55 #end if
|
|
|
56 gffread $input
|
|
|
57 #if $reference_genome.source == 'cached':
|
|
|
58 -g "${reference_genome.fasta_indexes.fields.path}"
|
|
|
59 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
|
|
|
60 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
|
|
|
61 #end if
|
|
|
62 #elif $reference_genome.source == 'history':
|
|
|
63 -g genomeref.fa
|
|
|
64 #if $reference_genome.ref_filtering and str($reference_genome.ref_filtering) != '':
|
|
|
65 #echo ' '.join(str($reference_genome.ref_filtering).split(','))
|
|
|
66 #end if
|
|
|
67 #end if
|
|
|
68 #if $filtering and str($filtering) != '':
|
|
|
69 #echo " "
|
|
|
70 #echo ' '.join(str($filtering).split(','))
|
|
|
71 #end if
|
|
|
72 #if $maxintron and $maxintron > 0:
|
|
|
73 -i $maxintron
|
|
|
74 #end if
|
|
|
75 #if $region.region_filter == 'filter':
|
|
|
76 -r $region.range $region.discard_partial
|
|
|
77 #end if
|
|
|
78 #if $merging.merge_sel != 'none':
|
|
|
79 $merging.merge_cmd
|
|
|
80 #echo ' '.join(str($merging.merge_options).split(','))
|
|
|
81 #end if
|
|
|
82 #if $chr_replace:
|
|
|
83 -m "$chr_replace"
|
|
|
84 #end if
|
|
|
85 ## Does not seem to actually be used in the gffread code
|
|
|
86 ## #if $seq_info:
|
|
|
87 ## -A -s "$seq_info"
|
|
|
88 ## #end if
|
|
|
89 ## outputs
|
|
|
90 #if $reference_genome.source != 'none':
|
|
|
91 #if $reference_genome.fa_outputs and str($reference_genome.fa_outputs) != '':
|
|
|
92 #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(','))
|
|
|
93 #end if
|
|
|
94 #end if
|
|
|
95 #if $gffs.gff_fmt != 'none':
|
|
|
96 #if $gffs.tname:
|
|
|
97 -t "$gffs.tname"
|
|
|
98 #end if
|
|
|
99 #if $gffs.gff_fmt == 'gff':
|
|
|
100 #if $input.datatype.file_ext == 'gft':
|
|
|
101 $gffs.ensembl
|
|
|
102 #end if
|
|
|
103 $gffs.output_cmd
|
|
|
104 #elif $gffs.gff_fmt == 'gtf':
|
|
|
105 $gffs.output_cmd
|
|
|
106 #end if
|
|
|
107 #end if
|
|
|
108 ]]>
|
|
|
109 </command>
|
|
|
110 <inputs>
|
|
|
111 <param name="input" type="data" format="gff3,gtf" label="Input GFF3 or GTF feature file"/>
|
|
|
112 <!-- filtering -->
|
|
|
113 <param name="filtering" type="select" display="checkboxes" multiple="true" label="filters">
|
|
|
114 <option value="-U">(-U) discard single-exon transcripts</option>
|
|
|
115 <option value="-C">(-C) coding only: discard mRNAs that have no CDS feature</option>
|
|
|
116 <option value="-G">(-G) only parse additional exon attributes from the first exon and move them to the mRNA level (useful for GTF input)</option>
|
|
|
117 <option value="-O">(-O) process also non-transcript GFF records (by default non-transcript records are ignored)</option>
|
|
|
118 <option value="--no-pseudo">(--no-pseudo) filter out records matching the 'pseudo' keyword</option>
|
|
|
119 </param>
|
|
|
120 <conditional name="region">
|
|
|
121 <param name="region_filter" type="select" label="Filter by genome region">
|
|
|
122 <option value="none">No</option>
|
|
|
123 <option value="filter">Yes</option>
|
|
|
124 </param>
|
|
|
125 <when value="none"/>
|
|
|
126 <when value="filter">
|
|
|
127 <param name="range" type="text" value="" label="Only show transcripts overlapping coordinate range"
|
|
|
128 help="-r [['strand']'chr':]'start'..'end' <br> examples: <br> 1000..500000 <br> chr1:1000..500000 <br> +chr1:1000..500000 <br> -chr1:1000..500000" >
|
|
|
129 <validator type="regex">(([+-])?(\w+:))?\d+\.\.\d+</validator>
|
|
|
130 </param>
|
|
|
131 <param name="discard_partial" type="boolean" truevalue="-R" falsevalue="" check="false"
|
|
|
132 label="(-R) and discard all transcripts that are not fully contained within the given range"/>
|
|
|
133 </when>
|
|
|
134 </conditional>
|
|
|
135 <param name="maxintron" type="integer" value="" optional="true" min="0" label="(-i) max_intron - Filter out transcipts with large introns"
|
|
|
136 help="If set, discard transcripts having an intron larger"/>
|
|
|
137 <param name="chr_replace" type="data" format="tabular" optional="true" label="Replace reference sequence names (e.g. chr1 with 1)" >
|
|
|
138 <help>(-m chr_replace) <br>
|
|
|
139 chr_replace is input file is a 2 column tab-delimited file containing a reference (genomic) sequence replacement table with this format: <br>
|
|
|
140 "original_ref_ID" "new_ref_ID" <br>
|
|
|
141 GFF records on reference sequences that are not found among the "original_ref_ID" entries in this file will be filtered out
|
|
|
142 </help>
|
|
|
143 </param>
|
|
|
144
|
|
|
145 <!-- Does not appear to be used in the gffread code
|
|
|
146 <param name="seq_info" type="data" format="tabular" optional="true" label="Use the description field as the value for a 'descr' attribute to the GFF record">
|
|
|
147 <help>
|
|
|
148 (-s seq_info.fsize -A) useful with mRNA/EST/protein mappings <br>
|
|
|
149 seq_info input file is a 3 column tab-delimited file providing this info for each of the mapped sequences: <br>
|
|
|
150 "seq-name" "seq-length" "seq-description" <br>
|
|
|
151 </help>
|
|
|
152 </param>
|
|
|
153 -->
|
|
|
154
|
|
|
155 <!-- merging -->
|
|
|
156 <conditional name="merging">
|
|
|
157 <param name="merge_sel" type="select" label="(-M) Transcript merging">
|
|
|
158 <option value="none">none</option>
|
|
|
159 <option value="merge">merge: cluster the input transcripts into loci, collapsing matching transcripts</option>
|
|
|
160 <option value="cluster">cluster-only: merge but without collapsing matching transcripts</option>
|
|
|
161 </param>
|
|
|
162 <when value="none"/>
|
|
|
163 <when value="merge">
|
|
|
164 <param name="merge_cmd" type="hidden" value="--merge"/>
|
|
|
165 <expand macro="merge_opt_sel" />
|
|
|
166 </when>
|
|
|
167 <when value="cluster">
|
|
|
168 <param name="merge_cmd" type="hidden" value="--cluster-only"/>
|
|
|
169 <expand macro="cluster_opt_sel" />
|
|
|
170 </when>
|
|
|
171 </conditional>
|
|
|
172 <!-- reference sequence file -->
|
|
|
173 <!-- Error: -g option is required for options -w, -x, -y, -V, -N, -M -->
|
|
|
174 <conditional name="reference_genome">
|
|
|
175 <param name="source" type="select" label="(-g) Reference Genome (Required for fasta outputs)">
|
|
|
176 <option value="none">none</option>
|
|
|
177 <option value="cached"></option>
|
|
|
178 <option value="history">From your history</option>
|
|
|
179 </param>
|
|
|
180 <when value="none">
|
|
|
181 </when>
|
|
|
182 <when value="cached">
|
|
|
183 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
|
|
|
184 <options from_data_table="all_fasta"/>
|
|
|
185 </param>
|
|
|
186 <expand macro="ref_filtering_select" />
|
|
|
187 <expand macro="fasta_output_select" />
|
|
|
188 </when>
|
|
|
189 <when value="history">
|
|
|
190 <param name="genome_fasta" type="data" format="fasta" label="Genome Reference Fasta"/>
|
|
|
191 <expand macro="ref_filtering_select" />
|
|
|
192 <expand macro="fasta_output_select" />
|
|
|
193 </when>
|
|
|
194 </conditional>
|
|
|
195
|
|
|
196 <!-- outputs -->
|
|
|
197 <conditional name="gffs">
|
|
|
198 <param name="gff_fmt" type="select" optional="true" label="(-o) Feature File Output">
|
|
|
199 <option value="none">none</option>
|
|
|
200 <option value="gff">GFF</option>
|
|
|
201 <option value="gtf">GTF</option>
|
|
|
202 </param>
|
|
|
203 <when value="none">
|
|
|
204 </when>
|
|
|
205 <when value="gff">
|
|
|
206 <param name="output_cmd" type="hidden" value="-o output.gff3"/>
|
|
|
207 <param name="ensembl" type="boolean" truevalue="-F" falsevalue="" check="false" label="(-L) Ensembl GTF to GFF3 conversion"/>
|
|
|
208 <expand macro="trackname" />
|
|
|
209 </when>
|
|
|
210 <when value="gtf">
|
|
|
211 <param name="output_cmd" type="hidden" value="-T -o output.gtf"/>
|
|
|
212 <expand macro="trackname" />
|
|
|
213 </when>
|
|
|
214 </conditional>
|
|
|
215
|
|
|
216 <param name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" check="false"
|
|
|
217 label="(-F) full GFF attribute preservation (all attributes are shown)"/>
|
|
|
218 <param name="decode_url" type="boolean" truevalue="-D" falsevalue="" check="false"
|
|
|
219 label="(-D) decode url encoded characters within attributes"/>
|
|
|
220 <param name="expose" type="boolean" truevalue="-E" falsevalue="" check="false"
|
|
|
221 label="(-E) warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records"/>
|
|
|
222
|
|
|
223 </inputs>
|
|
|
224 <outputs>
|
|
|
225 <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff3">
|
|
|
226 <filter>gffs['gff_fmt'] == 'gff'</filter>
|
|
|
227 </data>
|
|
|
228 <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf">
|
|
|
229 <filter>gffs['gff_fmt'] == 'gtf'</filter>
|
|
|
230 </data>
|
|
|
231 <data name="output_exons" format="fasta" label="${tool.name} on ${on_string}: exons.fa" from_work_dir="exons.fa">
|
|
|
232 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('exons.fa') > 0 </filter>
|
|
|
233 </data>
|
|
|
234 <data name="output_cds" format="fasta" label="${tool.name} on ${on_string}: cds.fa" from_work_dir="cds.fa">
|
|
|
235 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('cds.fa') > 0</filter>
|
|
|
236 </data>
|
|
|
237 <data name="output_pep" format="fasta" label="${tool.name} on ${on_string}: pep.fa" from_work_dir="pep.fa">
|
|
|
238 <filter>'fa_outputs' in reference_genome and str(reference_genome['fa_outputs']).find('pep.fa') > 0</filter>
|
|
|
239 </data>
|
|
|
240 <data name="output_dupinfo" format="txt" label="${tool.name} on ${on_string}: dupinfo" from_work_dir="dupinfo">
|
|
|
241 <filter>'merge_options' in merging and merging['merge_options'].find('dupinfo') > 0</filter>
|
|
|
242 </data>
|
|
|
243 </outputs>
|
|
|
244 <tests>
|
|
|
245 <test>
|
|
|
246 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
|
|
|
247 <param name="gff_fmt" value="gff"/>
|
|
|
248 <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" />
|
|
|
249 </test>
|
|
|
250
|
|
|
251 <test>
|
|
|
252 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
|
|
|
253 <param name="filtering" value="--no-pseudo"/>
|
|
|
254 <param name="gff_fmt" value="gtf"/>
|
|
|
255 <output name="output_gtf">
|
|
|
256 <assert_contents>
|
|
|
257 <not_has_text text="pseudo" />
|
|
|
258 </assert_contents>
|
|
|
259 </output>
|
|
|
260 </test>
|
|
|
261
|
|
|
262 <test>
|
|
|
263 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
|
|
|
264 <param name="region_filter" value="filter"/>
|
|
|
265 <param name="range" value="19:496500..504965"/>
|
|
|
266 <param name="gff_fmt" value="gtf"/>
|
|
|
267 <output name="output_gtf">
|
|
|
268 <assert_contents>
|
|
|
269 <has_text text="ENST00000587541" />
|
|
|
270 <has_text text="ENST00000382683" />
|
|
|
271 </assert_contents>
|
|
|
272 </output>
|
|
|
273 </test>
|
|
|
274
|
|
|
275 <test>
|
|
|
276 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
|
|
|
277 <param name="region_filter" value="filter"/>
|
|
|
278 <param name="range" value="19:496500..504965"/>
|
|
|
279 <param name="discard_partial" value="true"/>
|
|
|
280 <param name="gff_fmt" value="gtf"/>
|
|
|
281 <output name="output_gtf">
|
|
|
282 <assert_contents>
|
|
|
283 <has_text text="ENST00000587541" />
|
|
|
284 <has_text text="ENST00000382683" />
|
|
|
285 </assert_contents>
|
|
|
286 </output>
|
|
|
287 </test>
|
|
|
288
|
|
|
289 <test>
|
|
|
290 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
|
|
|
291 <param name="filtering" value="-C"/>
|
|
|
292 <param name="region_filter" value="filter"/>
|
|
|
293 <param name="range" value="19:496500..504965"/>
|
|
|
294 <param name="gff_fmt" value="gtf"/>
|
|
|
295 <output name="output_gtf">
|
|
|
296 <assert_contents>
|
|
|
297 <not_has_text text="ENST00000587541" />
|
|
|
298 <has_text text="ENST00000382683" />
|
|
|
299 </assert_contents>
|
|
|
300 </output>
|
|
|
301 </test>
|
|
|
302
|
|
|
303 <test>
|
|
|
304 <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/>
|
|
|
305 <param name="source" value="history"/>
|
|
|
306 <param name="genome_fasta" ftype="fasta" value="Homo_sapiens.GRCh37.71.dna.chromosome.19.fa"/>
|
|
|
307 <param name="fa_outputs" value="-w exons.f,-x cds.fa,-y pep.fa"/>
|
|
|
308 <param name="region_filter" value="filter"/>
|
|
|
309 <param name="range" value="19:496500..504965"/>
|
|
|
310 <param name="gff_fmt" value="gtf"/>
|
|
|
311 <output name="output_gtf">
|
|
|
312 <assert_contents>
|
|
|
313 <not_has_text text="ENST00000587541" />
|
|
|
314 <has_text text="ENST00000382683" />
|
|
|
315 </assert_contents>
|
|
|
316 </output>
|
|
|
317 <output name="output_exons">
|
|
|
318 <assert_contents>
|
|
|
319 <has_text text="ENST00000346144 gene=MADCAM1 CDS=47-932" />
|
|
|
320 <has_text text="CTATTTAAGCGGCTTCCCCGCGGCCTCGGGACAGAGGGGACTGAGCATGGATTTCGGACTGGCCCTCCTG" />
|
|
|
321 </assert_contents>
|
|
|
322 </output>
|
|
|
323 <output name="output_cds">
|
|
|
324 <assert_contents>
|
|
|
325 <has_text text="ENST00000346144 gene=MADCAM1" />
|
|
|
326 <has_text text="ATGGATTTCGGACTGGCCCTCCTGCTGGCGGGGCTTCTGGGGCTCCTCCTCGGCCAGTCCCTCCAGGTGA" />
|
|
|
327 </assert_contents>
|
|
|
328 </output>
|
|
|
329 <output name="output_pep">
|
|
|
330 <assert_contents>
|
|
|
331 <has_text text="ENST00000346144 gene=MADCAM1" />
|
|
|
332 <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" />
|
|
|
333 </assert_contents>
|
|
|
334 </output>
|
|
|
335 </test>
|
|
|
336
|
|
|
337 </tests>
|
|
|
338 <help>
|
|
|
339 <![CDATA[
|
|
|
340 **gffread Filters and/or converts GFF3/GTF2 records**
|
|
|
341
|
|
|
342 Usage: ::
|
|
|
343
|
|
|
344 gffread "input_gff" [-g "genomic_seqs_fasta" | "dir"][-s "seq_info.fsize"]
|
|
|
345 [-o "outfile.gff"] [-t "tname"] [-r [["strand"]"chr":]"start".."end" [-R]]
|
|
|
346 [-CTVNJMKQAFGUBHZWTOLE] [-w "exons.fa"] [-x "cds.fa"] [-y "tr_cds.fa"]
|
|
|
347 [-i "maxintron"]
|
|
|
348
|
|
|
349 Options: ::
|
|
|
350
|
|
|
351 -g full path to a multi-fasta file with the genomic sequences
|
|
|
352 for all input mappings, OR a directory with single-fasta files
|
|
|
353 (one per genomic sequence, with file names matching sequence names)
|
|
|
354 -s <seq_info.fsize> is a tab-delimited file providing this info
|
|
|
355 for each of the mapped sequences:
|
|
|
356 <seq-name> <seq-length> <seq-description>
|
|
|
357 (useful for -A option with mRNA/EST/protein mappings)
|
|
|
358 -i discard transcripts having an intron larger than <maxintron>
|
|
|
359 -r only show transcripts overlapping coordinate range <start>..<end>
|
|
|
360 (on chromosome/contig <chr>, strand <strand> if provided)
|
|
|
361 -R for -r option, discard all transcripts that are not fully
|
|
|
362 contained within the given range
|
|
|
363 -U discard single-exon transcripts
|
|
|
364 -C coding only: discard mRNAs that have no CDS feature
|
|
|
365 -F full GFF attribute preservation (all attributes are shown)
|
|
|
366 -G only parse additional exon attributes from the first exon
|
|
|
367 and move them to the mRNA level (useful for GTF input)
|
|
|
368 -A use the description field from <seq_info.fsize> and add it
|
|
|
369 as the value for a 'descr' attribute to the GFF record
|
|
|
370
|
|
|
371 -O process also non-transcript GFF records (by default non-transcript
|
|
|
372 records are ignored)
|
|
|
373 -V discard any mRNAs with CDS having in-frame stop codons
|
|
|
374 -H for -V option, check and adjust the starting CDS phase
|
|
|
375 if the original phase leads to a translation with an
|
|
|
376 in-frame stop codon
|
|
|
377 -B for -V option, single-exon transcripts are also checked on the
|
|
|
378 opposite strand
|
|
|
379 -N discard multi-exon mRNAs that have any intron with a non-canonical
|
|
|
380 splice site consensus (i.e. not GT-AG, GC-AG or AT-AC)
|
|
|
381 -J discard any mRNAs that either lack initial START codon
|
|
|
382 or the terminal STOP codon, or have an in-frame stop codon
|
|
|
383 (only print mRNAs with a fulll, valid CDS)
|
|
|
384 --no-pseudo: filter out records matching the 'pseudo' keyword
|
|
|
385
|
|
|
386 -M/--merge : cluster the input transcripts into loci, collapsing matching
|
|
|
387 transcripts (those with the same exact introns and fully contained)
|
|
|
388 -d <dupinfo> : for -M option, write collapsing info to file <dupinfo>
|
|
|
389 --cluster-only: same as --merge but without collapsing matching transcripts
|
|
|
390 -K for -M option: also collapse shorter, fully contained transcripts
|
|
|
391 with fewer introns than the container
|
|
|
392 -Q for -M option, remove the containment restriction:
|
|
|
393 (multi-exon transcripts will be collapsed if just their introns match,
|
|
|
394 while single-exon transcripts can partially overlap (80%))
|
|
|
395
|
|
|
396 --force-exons: make sure that the lowest level GFF features are printed as
|
|
|
397 "exon" features
|
|
|
398 -E expose (warn about) duplicate transcript IDs and other potential
|
|
|
399 problems with the given GFF/GTF records
|
|
|
400 -D decode url encoded characters within attributes
|
|
|
401 -Z merge close exons into a single exon (for intron size<4)
|
|
|
402 -w write a fasta file with spliced exons for each GFF transcript
|
|
|
403 -x write a fasta file with spliced CDS for each GFF transcript
|
|
|
404 -W for -w and -x options, also write for each fasta record the exon
|
|
|
405 coordinates projected onto the spliced sequence
|
|
|
406 -y write a protein fasta file with the translation of CDS for each record
|
|
|
407 -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)
|
|
|
408 -m <chr_replace> is a reference (genomic) sequence replacement table with
|
|
|
409 this format:
|
|
|
410 <original_ref_ID> <new_ref_ID>
|
|
|
411 GFF records on reference sequences that are not found among the
|
|
|
412 <original_ref_ID> entries in this file will be filtered out
|
|
|
413 -o the "filtered" GFF records will be written to <outfile.gff>
|
|
|
414 (use -o- for printing to stdout)
|
|
|
415 -t use <trackname> in the second column of each GFF output line
|
|
|
416 -T -o option will output GTF format instead of GFF3
|
|
|
417
|
|
|
418
|
|
|
419
|
|
|
420
|
|
|
421
|
|
|
422 ]]>
|
|
|
423 </help>
|
|
|
424 </tool>
|
