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comparison transdecoder.xml @ 6:a6a3e3be07bf draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder commit 2147ee46c226f99d16899eb29b223f0f80db5491"
author iuc
date Fri, 22 Oct 2021 11:14:38 +0000
parents a7df62d5e6d7
children
comparison
equal deleted inserted replaced
5:a7df62d5e6d7 6:a6a3e3be07bf
1 <tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="transdecoder" name="TransDecoder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>finds coding regions within transcripts</description> 2 <description>finds coding regions within transcripts</description>
3 <xrefs>
4 <xref type="bio.tools">TransDecoder</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <token name="@TOOL_VERSION@">5.5.0</token> 7 <token name="@TOOL_VERSION@">5.5.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 8 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 9 </macros>
7 <requirements> 10 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">transdecoder</requirement>
12 <requirement type="package" version="3.0">zip</requirement>
9 </requirements> 13 </requirements>
10 <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep 'TransDecoder.LongOrfs' | cut -f 2 -d ' ']]></version_command> 14 <version_command><![CDATA[TransDecoder.LongOrfs --version 2>&1 | grep 'TransDecoder.LongOrfs' | cut -f 2 -d ' ']]></version_command>
11 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
12 ## initialize 16 ## initialize
13 ln -s '${t}' 'transcripts.fasta' && 17 ln -s '${t}' 'transcripts.fasta' &&
50 54
51 ## postprocessing 55 ## postprocessing
52 #if 'log' in $oo.out 56 #if 'log' in $oo.out
53 |& tee '$out_log' 57 |& tee '$out_log'
54 #end if 58 #end if
59 && if ls 'output/'*'.pdf' >/dev/null 2>&1; then zip 'seqlogo.zip' 'output/'*'.pdf' -q -j; fi
55 ]]></command> 60 ]]></command>
56 <inputs> 61 <inputs>
57 <param argument="-t" type="data" format="fasta" label="Select file with transcripts"/> 62 <param argument="-t" type="data" format="fasta" label="Select file with transcripts"/>
58 <param argument="-G" type="select" label="Select genetic code"> 63 <param argument="-G" type="select" label="Select genetic code">
59 <option value="Acetabularia">Acetabularia</option> 64 <option value="Acetabularia">Acetabularia</option>
82 <option value="Universal" selected="true">Universal</option> 87 <option value="Universal" selected="true">Universal</option>
83 </param> 88 </param>
84 <section name="lo" title="LongOrfs options" expanded="true"> 89 <section name="lo" title="LongOrfs options" expanded="true">
85 <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Select gene-to-transcript identifier mapping file" help="gene_id&lt;tab&gt;trans_id&lt;return&gt;"/> 90 <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Select gene-to-transcript identifier mapping file" help="gene_id&lt;tab&gt;trans_id&lt;return&gt;"/>
86 <param argument="-m" type="integer" value="100" min="1" label="Set minimum protein length"/> 91 <param argument="-m" type="integer" value="100" min="1" label="Set minimum protein length"/>
87 <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand."/> 92 <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Activate strand-specificity?" help="Only analyse top strand?"/>
88 </section> 93 </section>
89 <section name="po" title="Predict options" expanded="true"> 94 <section name="po" title="Predict options" expanded="true">
90 <!-- 95 <!--
91 TransDecoder.Predict can be skipped if only longest_orfs.pep (as a result of TransDecoder.LongOrfs) is required, e.g. for homology search via BlastP and Pfam. 96 TransDecoder.Predict can be skipped if only longest_orfs.pep (as a result of TransDecoder.LongOrfs) is required, e.g. for homology search via BlastP and Pfam.
92 --> 97 -->
104 <when value="dynamic"/> 109 <when value="dynamic"/>
105 <when value="strict"> 110 <when value="strict">
106 <param argument="--retain_long_orfs_length" type="integer" value="1000000" min="0" label="Set long ORFs length" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding."/> 111 <param argument="--retain_long_orfs_length" type="integer" value="1000000" min="0" label="Set long ORFs length" help="Retain all ORFs found that are equal or longer than these many nucleotides even if no other evidence marks it as coding."/>
107 </when> 112 </when>
108 </conditional> 113 </conditional>
109 <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (outfmt 6 format)"/> 114 <param argument="--retain_blastp_hits" type="data" format="tabular" optional="true" label="Select BlastP result file" help="Any ORF with a blast match will be retained in the final output. (tabular outfmt6 file)"/>
110 <param argument="--retain_pfam_hits" type="data" format="tabular" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (domtblout file)"/> 115 <param argument="--retain_pfam_hits" type="data" format="txt" optional="true" label="Select Pfam result file" help="Domain table output file from running hmmscan to search Pfam. Any ORF with a pfam domain hit will be retained in the final output. (tabular domtblout file)"/>
111 <param argument="--single_best_only" type="boolean" truevalue="--single_best_only" falsevalue="" label="Retain only the single best ORF per transcript?" help="Prioritized by homology than ORF length."/> 116 <param argument="--single_best_only" type="boolean" truevalue="--single_best_only" falsevalue="" label="Retain only the single best ORF per transcript?" help="Prioritized by homology than ORF length."/>
112 <param argument="--no_refine_starts" type="boolean" truevalue="--no_refine_starts" falsevalue="" label="Start refinement that identifies potential start codons for 5' partial ORFs using a PWM?"/> 117 <param argument="--no_refine_starts" type="boolean" truevalue="--no_refine_starts" falsevalue="" label="Start refinement that identifies potential start codons for 5' partial ORFs using a PWM?"/>
113 <param argument="-T" type="integer" value="500" min="1" label="Set top longest ORFs to train Markov Model" help="The first (10*value) elements are selected for removing redundancies. Then number of longst ORFs of this value are selected from the non-redundant set."/> 118 <param argument="-T" type="integer" value="500" min="1" label="Set top longest ORFs to train Markov Model" help="The first (10*value) elements are selected for removing redundancies. Then number of longst ORFs of this value are selected from the non-redundant set."/>
114 </when> 119 </when>
115 <when value="no"/> 120 <when value="no"/>
116 </conditional> 121 </conditional>
117 </section> 122 </section>
118 <section name="oo" title="Output options"> 123 <section name="oo" title="Output options" expanded="true">
119 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific NOVOplasty run."> 124 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)" help="Only shown in history if selected here and generated by the specific run.">
120 <!-- LongOrfs --> 125 <!-- LongOrfs -->
121 <option value="lo_cds">Longest ORFs (CDS)</option> 126 <option value="lo_cds">Longest ORFs (CDS)</option>
122 <option value="lo_gff3">Longest ORFs (GFF3)</option> 127 <option value="lo_gff3">Longest ORFs (GFF3)</option>
123 <option value="lo_pep" selected="true">Longest ORFs (PEP)</option> 128 <option value="lo_pep" selected="true">Longest ORFs (PEP)</option>
124 <!-- Predict --> 129 <!-- Predict -->
125 <option value="bed" selected="true">Results (BED)</option> 130 <option value="bed" selected="true">Results (BED)</option>
126 <option value="cds" selected="true">Results (CDS)</option> 131 <option value="cds" selected="true">Results (CDS)</option>
127 <option value="gff3" selected="true">Results (GFF3)</option> 132 <option value="gff3" selected="true">Results (GFF3)</option>
128 <option value="pep" selected="true">Results (PEP)</option> 133 <option value="pep" selected="true">Results (PEP)</option>
134 <option value="plot">Plots</option>
129 <!-- Others --> 135 <!-- Others -->
130 <option value="log">Log</option> 136 <option value="log">Log</option>
131 </param> 137 </param>
132 </section> 138 </section>
133 </inputs> 139 </inputs>
153 <filter>'gff3' in oo['out'] and po['predict_cond']['predict_sel'] =='yes'</filter> 159 <filter>'gff3' in oo['out'] and po['predict_cond']['predict_sel'] =='yes'</filter>
154 </data> 160 </data>
155 <data name="out_pep" format="fasta" from_work_dir="transcripts.fasta.transdecoder.pep" label="${tool.name} on ${on_string}: Results (PEP/FASTA)"> 161 <data name="out_pep" format="fasta" from_work_dir="transcripts.fasta.transdecoder.pep" label="${tool.name} on ${on_string}: Results (PEP/FASTA)">
156 <filter>'pep' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter> 162 <filter>'pep' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter>
157 </data> 163 </data>
164 <data name="out_plot" format="zip" from_work_dir="seqlogo.zip" label="${tool.name} on ${on_string}: Plots">
165 <filter>'plot' in oo['out'] and po['predict_cond']['predict_sel'] == 'yes'</filter>
166 </data>
158 <!-- Others --> 167 <!-- Others -->
159 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> 168 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
160 <filter>'log' in oo['out']</filter> 169 <filter>'log' in oo['out']</filter>
161 </data> 170 </data>
162 </outputs> 171 </outputs>
163 <tests> 172 <tests>
164 <!-- no test implemented for: gene_trans_map, retain_blastp_hits, retain_pfam_hits -->
165
166 <!-- #1 default --> 173 <!-- #1 default -->
167 <test expect_num_outputs="5"> 174 <test expect_num_outputs="5">
168 <param name="t" value="transcripts.fasta"/> 175 <param name="t" value="transcripts.fasta"/>
169 <!-- LongOrfs --> 176 <!-- LongOrfs -->
170 <output name="out_lo_pep"> 177 <output name="out_lo_pep">
171 <assert_contents> 178 <assert_contents>
172 <has_n_lines n="772"/> 179 <has_n_lines n="190"/>
173 <has_text_matching expression=".+comp874.+"/> 180 <has_line line=">CUFF.20.1.p2 type:3prime_partial len:205 gc:Universal CUFF.20.1:612-1(-)"/>
174 </assert_contents> 181 </assert_contents>
175 </output> 182 </output>
176 <!-- Predict --> 183 <!-- Predict -->
177 <output name="out_bed"> 184 <output name="out_bed">
178 <assert_contents> 185 <assert_contents>
179 <has_n_lines n="337"/> 186 <has_n_lines n="81"/>
180 <has_text_matching expression="comp98\_c0\_seq1.+"/> 187 <has_text_matching expression="CUFF\.9\.1.+"/>
181 </assert_contents> 188 </assert_contents>
182 </output> 189 </output>
183 <output name="out_cds"> 190 <output name="out_cds">
184 <assert_contents> 191 <assert_contents>
185 <has_n_lines n="6959"/> 192 <has_n_lines n="1578"/>
186 <has_text_matching expression=">comp98\_c0\_seq1.+"/> 193 <has_line line=">CUFF.9.1.p1 GENE.CUFF.9.1~~CUFF.9.1.p1 ORF type:complete len:156 (+),score=36.30 CUFF.9.1:173-640(+)"/>
187 </assert_contents> 194 </assert_contents>
188 </output> 195 </output>
189 <output name="out_gff3"> 196 <output name="out_gff3">
190 <assert_contents> 197 <assert_contents>
191 <has_n_lines n="2165"/> 198 <has_n_lines n="542"/>
192 <has_text_matching expression="comp98\_c0\_seq1.+"/> 199 <has_text_matching expression="CUFF\.9\.1.+"/>
193 </assert_contents> 200 </assert_contents>
194 </output> 201 </output>
195 <output name="out_pep"> 202 <output name="out_pep">
196 <assert_contents> 203 <assert_contents>
197 <has_n_lines n="2644"/> 204 <has_n_lines n="608"/>
198 <has_text_matching expression="comp98\_c0\_seq1.+"/> 205 <has_text_matching expression="CUFF\.9\.1.+"/>
199 </assert_contents> 206 </assert_contents>
200 </output> 207 </output>
201 </test> 208 </test>
202 <!-- #2 --> 209 <!-- #2 -->
203 <test expect_num_outputs="8"> 210 <test expect_num_outputs="9">
204 <param name="t" value="transcripts.fasta"/> 211 <param name="t" value="transcripts.fasta"/>
205 <param name="G" value="Acetabularia"/> 212 <param name="G" value="Acetabularia"/>
206 <section name="lo"> 213 <section name="lo">
207 <param name="m" value="101"/> 214 <param name="m" value="101"/>
208 <param name="S" value="true"/> 215 <param name="S" value="true"/>
209 </section> 216 </section>
210 <section name="po">
211 <conditional name="predict_cond">
212 <param name="predict_sel" value="yes"/>
213 <conditional name="mode_cond">
214 <param name="mode_sel" value="dynamic"/>
215 </conditional>
216 <param name="single_best_only" value="true"/>
217 <param name="no_refine_starts" value="true"/>
218 <param name="T" value="501"/>
219 </conditional>
220 </section>
221 <section name="oo">
222 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,log"/>
223 </section>
224 <!-- LongOrfs -->
225 <output name="out_lo_cds">
226 <assert_contents>
227 <has_n_lines n="1454"/>
228 <has_text_matching expression=">comp874\_c0\_seq1.+"/>
229 </assert_contents>
230 </output>
231 <output name="out_lo_gff3">
232 <assert_contents>
233 <has_n_lines n="4565"/>
234 <has_text_matching expression="comp874\_c0\_seq1.+"/>
235 </assert_contents>
236 </output>
237 <output name="out_lo_pep">
238 <assert_contents>
239 <has_n_lines n="1454"/>
240 <has_text_matching expression=">comp874\_c0\_seq1.+"/>
241 </assert_contents>
242 </output>
243 <!-- Predict -->
244 <output name="out_bed">
245 <assert_contents>
246 <has_n_lines n="340"/>
247 <has_text_matching expression="comp98\_c0\_seq1.+"/>
248 </assert_contents>
249 </output>
250 <output name="out_cds">
251 <assert_contents>
252 <has_n_lines n="7512"/>
253 <has_text_matching expression=">comp98\_c0\_seq1.+"/>
254 </assert_contents>
255 </output>
256 <output name="out_gff3">
257 <assert_contents>
258 <has_n_lines n="2000"/>
259 <has_text_matching expression="comp98\_c0\_seq1.+"/>
260 </assert_contents>
261 </output>
262 <output name="out_pep">
263 <assert_contents>
264 <has_n_lines n="2833"/>
265 <has_text_matching expression=">comp98\_c0\_seq1.+"/>
266 </assert_contents>
267 </output>
268 <!-- Others -->
269 <output name="out_log">
270 <assert_contents>
271 <has_text_matching expression="transdecoder is finished.+"/>
272 </assert_contents>
273 </output>
274 </test>
275 <!-- #3 -->
276 <test expect_num_outputs="8">
277 <param name="t" value="transcripts.fasta"/>
278 <section name="po"> 217 <section name="po">
279 <conditional name="predict_cond"> 218 <conditional name="predict_cond">
280 <param name="predict_sel" value="yes"/> 219 <param name="predict_sel" value="yes"/>
281 <conditional name="mode_cond"> 220 <conditional name="mode_cond">
282 <param name="mode_sel" value="strict"/> 221 <param name="mode_sel" value="strict"/>
283 <param name="retain_long_orfs_length" value="1000001"/> 222 <param name="retain_long_orfs_length" value="1000001"/>
284 </conditional> 223 </conditional>
224 <param name="retain_blastp_hits" value="blastp.outfmt6"/>
225 <param name="retain_pfam_hits" value="pfam.domtblout"/>
226 <param name="single_best_only" value="true"/>
227 <param name="no_refine_starts" value="true"/>
228 <param name="T" value="501"/>
285 </conditional> 229 </conditional>
286 </section> 230 </section>
287 <section name="oo"> 231 <section name="oo">
288 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,log"/> 232 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,plot,log"/>
289 </section> 233 </section>
290 <!-- LongOrfs --> 234 <!-- LongOrfs -->
291 <output name="out_lo_cds"> 235 <output name="out_lo_cds">
292 <assert_contents> 236 <assert_contents>
293 <has_n_lines n="772"/> 237 <has_n_lines n="398"/>
294 <has_text_matching expression=">comp874\_c0\_seq1.+"/> 238 <has_text_matching expression="CUFF\.20\.1.+"/>
295 </assert_contents> 239 </assert_contents>
296 </output> 240 </output>
297 <output name="out_lo_gff3"> 241 <output name="out_lo_gff3">
298 <assert_contents> 242 <assert_contents>
299 <has_n_lines n="2486"/> 243 <has_n_lines n="1330"/>
300 <has_text_matching expression="comp874\_c0\_seq1.+"/> 244 <has_text_matching expression="CUFF\.20\.1.+"/>
301 </assert_contents> 245 </assert_contents>
302 </output> 246 </output>
303 <output name="out_lo_pep"> 247 <output name="out_lo_pep">
304 <assert_contents> 248 <assert_contents>
305 <has_n_lines n="772"/> 249 <has_n_lines n="398"/>
306 <has_text_matching expression=">comp874\_c0\_seq1.+"/> 250 <has_text_matching expression="CUFF\.20\.1.+"/>
307 </assert_contents> 251 </assert_contents>
308 </output> 252 </output>
309 <!-- Predict --> 253 <!-- Predict -->
310 <output name="out_bed"> 254 <output name="out_bed">
311 <assert_contents> 255 <assert_contents>
312 <has_n_lines n="337"/> 256 <has_n_lines n="62"/>
313 <has_text_matching expression="comp98\_c0\_seq1.+"/> 257 <has_text_matching expression="CUFF\.9\.1.+"/>
314 </assert_contents> 258 </assert_contents>
315 </output> 259 </output>
316 <output name="out_cds"> 260 <output name="out_cds">
317 <assert_contents> 261 <assert_contents>
318 <has_n_lines n="6959"/> 262 <has_n_lines n="1312"/>
319 <has_text_matching expression=">comp98\_c0\_seq1.+"/> 263 <has_text_matching expression="CUFF\.9\.1.+"/>
320 </assert_contents> 264 </assert_contents>
321 </output> 265 </output>
322 <output name="out_gff3"> 266 <output name="out_gff3">
323 <assert_contents> 267 <assert_contents>
324 <has_n_lines n="2165"/> 268 <has_n_lines n="395"/>
325 <has_text_matching expression="comp98\_c0\_seq1.+"/> 269 <has_text_matching expression="CUFF\.9\.1.+"/>
326 </assert_contents> 270 </assert_contents>
327 </output> 271 </output>
328 <output name="out_pep"> 272 <output name="out_pep">
329 <assert_contents> 273 <assert_contents>
330 <has_n_lines n="2644"/> 274 <has_n_lines n="500"/>
331 <has_text_matching expression=">comp98\_c0\_seq1.+"/> 275 <has_text_matching expression="CUFF\.9\.1.+"/>
276 </assert_contents>
277 </output>
278 <output name="out_plot">
279 <assert_contents>
280 <has_size value="0"/>
281 </assert_contents>
282 </output>
283 <!-- Others -->
284 <output name="out_log">
285 <assert_contents>
286 <has_text_matching expression="transdecoder is finished.+"/>
287 </assert_contents>
288 </output>
289 </test>
290 <!-- #3 -->
291 <test expect_num_outputs="9">
292 <param name="t" value="pasa_assemblies.fasta"/>
293 <section name="lo">
294 <param name="gene_trans_map" value="pasa_genetransmap.txt"/>
295 </section>
296 <section name="oo">
297 <param name="out" value="lo_pep,lo_gff3,lo_cds,bed,cds,gff3,pep,plot,log"/>
298 </section>
299 <!-- LongOrfs -->
300 <output name="out_lo_cds">
301 <assert_contents>
302 <has_n_lines n="534"/>
303 <has_text_matching expression=">asmbl\_236\.p1.+"/>
304 </assert_contents>
305 </output>
306 <output name="out_lo_gff3">
307 <assert_contents>
308 <has_n_lines n="1742"/>
309 <has_text_matching expression="asmbl\_236.+"/>
310 </assert_contents>
311 </output>
312 <output name="out_lo_pep">
313 <assert_contents>
314 <has_n_lines n="534"/>
315 <has_text_matching expression=">asmbl\_236\.p1.+"/>
316 </assert_contents>
317 </output>
318 <!-- Predict -->
319 <output name="out_bed">
320 <assert_contents>
321 <has_n_lines n="204"/>
322 <has_text_matching expression="asmbl\_99.+"/>
323 </assert_contents>
324 </output>
325 <output name="out_cds">
326 <assert_contents>
327 <has_n_lines n="3560"/>
328 <has_text_matching expression=">asmbl\_99\.p1.+"/>
329 </assert_contents>
330 </output>
331 <output name="out_gff3">
332 <assert_contents>
333 <has_n_lines n="1337"/>
334 <has_text_matching expression="asmbl\_99.+"/>
335 </assert_contents>
336 </output>
337 <output name="out_pep">
338 <assert_contents>
339 <has_n_lines n="1391"/>
340 <has_text_matching expression=">asmbl\_99\.p1.+"/>
341 </assert_contents>
342 </output>
343 <output name="out_plot">
344 <assert_contents>
345 <has_size value="714868" delta="1000"/>
332 </assert_contents> 346 </assert_contents>
333 </output> 347 </output>
334 <!-- Others --> 348 <!-- Others -->
335 <output name="out_log"> 349 <output name="out_log">
336 <assert_contents> 350 <assert_contents>
345 <conditional name="predict_cond"> 359 <conditional name="predict_cond">
346 <param name="predict_sel" value="no"/> 360 <param name="predict_sel" value="no"/>
347 </conditional> 361 </conditional>
348 </section> 362 </section>
349 <!-- LongOrfs --> 363 <!-- LongOrfs -->
350 <output name="out_lo_pep"> 364 <output name="out_pep">
351 <assert_contents> 365 <assert_contents>
352 <has_n_lines n="772"/> 366 <has_n_lines n="190"/>
353 <has_text_matching expression="c"/> 367 <has_text_matching expression="CUFF\.9\.1.+"/>
354 </assert_contents> 368 </assert_contents>
355 </output> 369 </output>
356 </test> 370 </test>
357 </tests> 371 </tests>
358 <help><![CDATA[ 372 <help><![CDATA[
401 415
402 - Results (PEP/FASTA): peptide sequences for the final candidate ORFs; all shorter candidates within longer ORFs were removed 416 - Results (PEP/FASTA): peptide sequences for the final candidate ORFs; all shorter candidates within longer ORFs were removed
403 - Results (CDS/FASTA): nucleotide sequences for coding regions of the final candidate ORFs 417 - Results (CDS/FASTA): nucleotide sequences for coding regions of the final candidate ORFs
404 - Results (GFF3): positions within the target transcripts of the final selected ORFs 418 - Results (GFF3): positions within the target transcripts of the final selected ORFs
405 - Results (BED): BED-formatted file describing ORF positions, best for viewing using GenomeView or IGV 419 - Results (BED): BED-formatted file describing ORF positions, best for viewing using GenomeView or IGV
420 - Plots: sequence logos and scores (compressed PDF)
406 421
407 *Other* 422 *Other*
408 423
409 - Log file 424 - Log file
410 425