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author jjohnson
date Sun, 28 Dec 2014 16:33:55 -0500
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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 &lt; 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' &lt;br&gt; examples: &lt;br&gt; 1000..500000 &lt;br&gt; chr1:1000..500000 &lt;br&gt; +chr1:1000..500000 &lt;br&gt; -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) &lt;br&gt;
139 chr_replace is input file is a 2 column tab-delimited file containing a reference (genomic) sequence replacement table with this format: &lt;br&gt;
140 "original_ref_ID" "new_ref_ID" &lt;br&gt;
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 &lt;br&gt;
149 seq_info input file is a 3 column tab-delimited file providing this info for each of the mapped sequences: &lt;br&gt;
150 "seq-name" "seq-length" "seq-description" &lt;br&gt;
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>