Mercurial > repos > iuc > gffcompare
comparison gffcompare.xml @ 4:0f710191a66d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
author | iuc |
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date | Thu, 17 Oct 2019 03:01:26 -0400 |
parents | 2bb86e2c417f |
children | f99dd58de04f |
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3:2bb86e2c417f | 4:0f710191a66d |
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1 <tool id="gffcompare" name="GffCompare" version="@GFFCOMPARE_VERSION@"> | 1 <tool id="gffcompare" name="GffCompare" version="@GFFCOMPARE_VERSION@"> |
2 <description>compare assembled transcripts to a reference annotation</description> | 2 <description>compare assembled transcripts to a reference annotation</description> |
3 <macros> | 3 <macros> |
4 <token name="@GFFCOMPARE_VERSION@">0.11.2</token> | 4 <token name="@GFFCOMPARE_VERSION@">0.11.2</token> |
5 </macros> | 5 </macros> |
6 <requirements> | 6 <requirements> |
7 <requirement type="package" version="@GFFCOMPARE_VERSION@">gffcompare</requirement> | 7 <requirement type="package" version="@GFFCOMPARE_VERSION@">gffcompare</requirement> |
8 </requirements> | 8 </requirements> |
9 <version_command>gffcompare -v | awk '{print $2}'</version_command> | 9 <version_command>gffcompare -v | awk '{print $2}'</version_command> |
10 <command detect_errors="aggressive"><![CDATA[ | 10 <command detect_errors="aggressive"><![CDATA[ |
11 #import re | 11 #import re |
47 -s ref_seq.fa | 47 -s ref_seq.fa |
48 #end if | 48 #end if |
49 | 49 |
50 $discard_single_exon | 50 $discard_single_exon |
51 $discard_duplicates | 51 $discard_duplicates |
52 $no_merge | |
52 -e $max_dist_exon | 53 -e $max_dist_exon |
53 -d $max_dist_group | 54 -d $max_dist_group |
54 $chr_stats | 55 $chr_stats |
55 -p '$adv_output.p' | 56 -p '$adv_output.p' |
56 $adv_output.A | 57 $adv_output.A |
77 <option value="history">History</option> | 78 <option value="history">History</option> |
78 </param> | 79 </param> |
79 <when value="cached"> | 80 <when value="cached"> |
80 <param argument="-r" label="Using reference annotation" name="index" type="select"> | 81 <param argument="-r" label="Using reference annotation" name="index" type="select"> |
81 <options from_data_table="gene_sets"> | 82 <options from_data_table="gene_sets"> |
82 <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" /> | 83 <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" /> |
83 </options> | 84 </options> |
84 <validator message="No reference annotation is available for the build associated with the selected input dataset" type="no_options" /> | 85 <validator message="No reference annotation is available for the build associated with the selected input dataset" type="no_options" /> |
85 </param> | 86 </param> |
86 </when> | 87 </when> |
87 <when value="history"> | 88 <when value="history"> |
115 <option value="history">History</option> | 116 <option value="history">History</option> |
116 </param> | 117 </param> |
117 <when value="cached"> | 118 <when value="cached"> |
118 <param argument="-s" label="Using reference genome" name="index" type="select"> | 119 <param argument="-s" label="Using reference genome" name="index" type="select"> |
119 <options from_data_table="fasta_indexes"> | 120 <options from_data_table="fasta_indexes"> |
120 <filter column="1" key="dbkey" ref="gffinputs" type="data_meta" /> | 121 <filter column="dbkey" key="dbkey" ref="gffinputs" type="data_meta" /> |
121 </options> | 122 </options> |
122 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> | 123 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> |
123 </param> | 124 </param> |
124 </when> | 125 </when> |
125 <when value="history"> | 126 <when value="history"> |
141 <param name="no_merge" argument="--no-merge" type="boolean" checked="false" truevalue="--no-merge" falsevalue="" label="Disable close-exon merging" help="Default: merge exons separated by 'introns' shorter than 5 bases" /> | 142 <param name="no_merge" argument="--no-merge" type="boolean" checked="false" truevalue="--no-merge" falsevalue="" label="Disable close-exon merging" help="Default: merge exons separated by 'introns' shorter than 5 bases" /> |
142 <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" /> | 143 <param argument="-e" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" label="Max. Distance for assessing exon accuracy" name="max_dist_exon" type="integer" value="100" /> |
143 <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" /> | 144 <param argument="-d" help="max. distance (range) for grouping transcript start sites. Default: 100" label="Max distance for transcript grouping" name="max_dist_group" type="integer" value="100" /> |
144 <param name="chr_stats" argument="--chr-stats" type="boolean" checked="false" truevalue="--chr-stats" falsevalue="" label="Show summary and accuracy data separately for each reference sequence in the transcript accuracy data set" /> | 145 <param name="chr_stats" argument="--chr-stats" type="boolean" checked="false" truevalue="--chr-stats" falsevalue="" label="Show summary and accuracy data separately for each reference sequence in the transcript accuracy data set" /> |
145 <section name="adv_output" title="Options for the combined GTF output file"> | 146 <section name="adv_output" title="Options for the combined GTF output file"> |
146 <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf (default: 'TCONS')" /> | 147 <param argument="-p" type="text" value="TCONS" label="name prefix for consensus transcripts" help="for combined.gtf" /> |
147 <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue="" label="discard matching and 'contained' transfrags" help="i.e. collapse intron-redundant transfrags across all query files" /> | 148 <param argument="-C" type="boolean" checked="false" truevalue="-C" falsevalue="" label="discard matching and 'contained' transfrags" help="i.e. collapse intron-redundant transfrags across all query files" /> |
148 <param argument="-A" type="boolean" checked="false" truevalue="-A" falsevalue="" label="discard the 'contained' transfrags except intron-redundant transfrags starting with a different 5' exon" help="like -C but does not discard intron-redundant transfrags if they start with a different 5' exon" /> | 149 <param argument="-A" type="boolean" checked="false" truevalue="-A" falsevalue="" label="discard the 'contained' transfrags except intron-redundant transfrags starting with a different 5' exon" help="like -C but does not discard intron-redundant transfrags if they start with a different 5' exon" /> |
149 <param argument="-X" type="boolean" checked="false" truevalue="-X" falsevalue="" label="discard the 'contained' transfrags also if ends stick out within the container's introns" help="like -C but also discard contained transfrags if transfrag ends stick out within the container's introns" /> | 150 <param argument="-X" type="boolean" checked="false" truevalue="-X" falsevalue="" label="discard the 'contained' transfrags also if ends stick out within the container's introns" help="like -C but also discard contained transfrags if transfrag ends stick out within the container's introns" /> |
150 <param argument="-K" type="boolean" checked="false" truevalue="-K" falsevalue="" label="do NOT discard any redundant transfrag matching a reference" help="for -C/-A/-X" /> | 151 <param argument="-K" type="boolean" checked="false" truevalue="-K" falsevalue="" label="do NOT discard any redundant transfrag matching a reference" help="for -C/-A/-X" /> |
151 </section> | 152 </section> |
182 <assert_command> | 183 <assert_command> |
183 <not_has_text text="-R " /> | 184 <not_has_text text="-R " /> |
184 <not_has_text text="-Q " /> | 185 <not_has_text text="-Q " /> |
185 <not_has_text text="--strict-match " /> | 186 <not_has_text text="--strict-match " /> |
186 <not_has_text text="-T " /> | 187 <not_has_text text="-T " /> |
187 <not_has_text text="-s " /> | 188 <has_text_matching expression="^.*gffcompare((?!-s).)*$" /> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is not set --> |
188 <not_has_text text="-M " /> | 189 <not_has_text text="-M " /> |
189 <not_has_text text="-N " /> | 190 <not_has_text text="-N " /> |
190 <has_text text="-e 100 " /> | 191 <has_text text="-e 100 " /> |
191 <has_text text="-d 100 " /> | 192 <has_text text="-d 100 " /> |
192 <not_has_text text="-D " /> | 193 <not_has_text text="-D " /> |
193 <not_has_text text="--no-merge " /> | 194 <not_has_text text="--no-merge " /> |
194 <has_text text="-p TCONS " /> | 195 <has_text text="-p 'TCONS' " /> |
195 <not_has_text text="-C " /> | 196 <not_has_text text="-C " /> |
196 <not_has_text text="-A " /> | 197 <not_has_text text="-A " /> |
197 <not_has_text text="-X " /> | 198 <not_has_text text="-X " /> |
198 <not_has_text text="-K " /> | 199 <not_has_text text="-K " /> |
199 </assert_command> | 200 </assert_command> |
219 </conditional> | 220 </conditional> |
220 <assert_command> | 221 <assert_command> |
221 <not_has_text text="-R " /> | 222 <not_has_text text="-R " /> |
222 <not_has_text text="-Q " /> | 223 <not_has_text text="-Q " /> |
223 <has_text text="-T " /> | 224 <has_text text="-T " /> |
224 <has_text text="-s " /> | 225 <has_text_matching expression="gffcompare.*-s " /> <!-- since ln also has -s a more complicated regexp is needed here to check if -s is set --> |
225 <not_has_text text="-M " /> | 226 <not_has_text text="-M " /> |
226 <not_has_text text="-N " /> | 227 <not_has_text text="-N " /> |
227 <has_text text="-e 100 " /> | 228 <has_text text="-e 100 " /> |
228 <has_text text="-d 100 " /> | 229 <has_text text="-d 100 " /> |
229 <has_text text="-p TCONS " /> | 230 <has_text text="-p 'TCONS' " /> |
230 <not_has_text text="-C " /> | 231 <not_has_text text="-C " /> |
231 <not_has_text text="-A " /> | 232 <not_has_text text="-A " /> |
232 <not_has_text text="-X " /> | 233 <not_has_text text="-X " /> |
233 <not_has_text text="-K " /> | 234 <not_has_text text="-K " /> |
234 </assert_command> | 235 </assert_command> |
253 </conditional> | 254 </conditional> |
254 <assert_command> | 255 <assert_command> |
255 <not_has_text text="-R " /> | 256 <not_has_text text="-R " /> |
256 <not_has_text text="-Q " /> | 257 <not_has_text text="-Q " /> |
257 <has_text text="-T " /> | 258 <has_text text="-T " /> |
258 <has_text text="-s " /> | 259 <has_text_matching expression="gffcompare.*-s " /> |
259 <not_has_text text="-M " /> | 260 <not_has_text text="-M " /> |
260 <not_has_text text="-N " /> | 261 <not_has_text text="-N " /> |
261 <has_text text="-e 100 " /> | 262 <has_text text="-e 100 " /> |
262 <has_text text="-d 100 " /> | 263 <has_text text="-d 100 " /> |
263 <has_text text="-p TCONS " /> | 264 <has_text text="-p 'TCONS' " /> |
264 <not_has_text text="-C " /> | 265 <not_has_text text="-C " /> |
265 <not_has_text text="-A " /> | 266 <not_has_text text="-A " /> |
266 <not_has_text text="-X " /> | 267 <not_has_text text="-X " /> |
267 <not_has_text text="-K " /> | 268 <not_has_text text="-K " /> |
268 </assert_command> | 269 </assert_command> |
285 <param name="use_seq_data" value="No" /> | 286 <param name="use_seq_data" value="No" /> |
286 </conditional> | 287 </conditional> |
287 <assert_command> | 288 <assert_command> |
288 <not_has_text text="-R " /> | 289 <not_has_text text="-R " /> |
289 <not_has_text text="-Q " /> | 290 <not_has_text text="-Q " /> |
291 <not_has_text text="--strict-match " /> | |
290 <not_has_text text="-T " /> | 292 <not_has_text text="-T " /> |
291 <not_has_text text="-M " /> | 293 <not_has_text text="-M " /> |
292 <not_has_text text="-N " /> | 294 <not_has_text text="-N " /> |
293 <has_text text="-e 100 " /> | 295 <has_text text="-e 100 " /> |
294 <has_text text="-d 100 " /> | 296 <has_text text="-d 100 " /> |
295 <has_text text="-p TCONS " /> | 297 <not_has_text text="-D " /> |
298 <not_has_text text="--no-merge " /> | |
299 <not_has_text text="--chr-stats" /> | |
300 <has_text text="-p 'TCONS' " /> | |
296 <not_has_text text="-C " /> | 301 <not_has_text text="-C " /> |
297 <not_has_text text="-A " /> | 302 <not_has_text text="-A " /> |
298 <not_has_text text="-X " /> | 303 <not_has_text text="-X " /> |
299 <not_has_text text="-K " /> | 304 <not_has_text text="-K " /> |
300 </assert_command> | 305 </assert_command> |
301 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" /> | 306 <output file="gffcompare_out2.stats" name="transcripts_stats" /> |
302 <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" /> | 307 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
303 <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> | 308 <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> |
304 <output file="gffcompare_out2.gtf" name="transcripts_combined" /> | 309 <output file="gffcompare_out2.gtf" name="transcripts_combined" /> |
305 <output_collection name="refmap_output" type="list" count="2"> | 310 <output_collection name="refmap_output" type="list" count="2"> |
306 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.refmap" ftype="tabular" /> | 311 <element name="gffcompare_in1_gtf" file="gffcompare_out2-1.refmap" ftype="tabular" /> |
307 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.refmap" ftype="tabular" /> | 312 <element name="gffcompare_in2_gtf" file="gffcompare_out2-2.refmap" ftype="tabular" /> |
344 <has_text text="-e 101 " /> | 349 <has_text text="-e 101 " /> |
345 <has_text text="-d 99 " /> | 350 <has_text text="-d 99 " /> |
346 <has_text text="-D " /> | 351 <has_text text="-D " /> |
347 <has_text text="--no-merge " /> | 352 <has_text text="--no-merge " /> |
348 <has_text text="--chr-stats" /> | 353 <has_text text="--chr-stats" /> |
349 <not_has_text text="-p TCONS " /> | 354 <has_text text="-p 'TCONS' " /> |
350 <not_has_text text="-C " /> | 355 <not_has_text text="-C " /> |
351 <not_has_text text="-A " /> | 356 <not_has_text text="-A " /> |
352 <not_has_text text="-X " /> | 357 <not_has_text text="-X " /> |
353 <not_has_text text="-K " /> | 358 <not_has_text text="-K " /> |
354 </assert_command> | 359 </assert_command> |
380 <param name="K" value="-K" /> | 385 <param name="K" value="-K" /> |
381 </section> | 386 </section> |
382 <assert_command> | 387 <assert_command> |
383 <not_has_text text="-R " /> | 388 <not_has_text text="-R " /> |
384 <not_has_text text="-Q " /> | 389 <not_has_text text="-Q " /> |
390 <not_has_text text="--strict-match " /> | |
385 <not_has_text text="-T " /> | 391 <not_has_text text="-T " /> |
386 <not_has_text text="-M " /> | 392 <not_has_text text="-M " /> |
387 <not_has_text text="-N " /> | 393 <not_has_text text="-N " /> |
388 <has_text text="-e 100 " /> | 394 <has_text text="-e 100 " /> |
389 <has_text text="-d 100 " /> | 395 <has_text text="-d 100 " /> |
390 <has_text text="-p OTHER " /> | 396 <not_has_text text="-D " /> |
397 <not_has_text text="--no-merge " /> | |
398 <not_has_text text="--chr-stats" /> | |
399 <has_text text="-p 'OTHER' " /> | |
391 <has_text text="-C " /> | 400 <has_text text="-C " /> |
392 <has_text text="-A " /> | 401 <has_text text="-A " /> |
393 <has_text text="-X " /> | 402 <has_text text="-X " /> |
394 <has_text text="-K " /> | 403 <has_text text="-K " /> |
395 </assert_command> | 404 </assert_command> |
414 <param name="use_seq_data" value="No" /> | 423 <param name="use_seq_data" value="No" /> |
415 </conditional> | 424 </conditional> |
416 <assert_command> | 425 <assert_command> |
417 <not_has_text text="-R " /> | 426 <not_has_text text="-R " /> |
418 <not_has_text text="-Q " /> | 427 <not_has_text text="-Q " /> |
428 <not_has_text text="--strict-match " /> | |
419 <has_text text="-T " /> | 429 <has_text text="-T " /> |
420 <not_has_text text="-M " /> | 430 <not_has_text text="-M " /> |
421 <not_has_text text="-N " /> | 431 <not_has_text text="-N " /> |
422 <has_text text="-e 100 " /> | 432 <has_text text="-e 100 " /> |
423 <has_text text="-d 100 " /> | 433 <has_text text="-d 100 " /> |
424 <has_text text="-p TCONS " /> | 434 <not_has_text text="-D " /> |
435 <not_has_text text="--no-merge " /> | |
436 <not_has_text text="--chr-stats" /> | |
437 <has_text text="-p 'TCONS' " /> | |
425 <not_has_text text="-C " /> | 438 <not_has_text text="-C " /> |
426 <not_has_text text="-A " /> | 439 <not_has_text text="-A " /> |
427 <not_has_text text="-X " /> | 440 <not_has_text text="-X " /> |
428 <not_has_text text="-K " /> | 441 <not_has_text text="-K " /> |
429 </assert_command> | 442 </assert_command> |
430 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="6" /> | 443 <output file="gffcompare_out2.stats" name="transcripts_stats" lines_diff="2" /> |
431 <output file="gffcompare_out2.loci" name="transcripts_loci" lines_diff="2" /> | 444 <output file="gffcompare_out2.loci" name="transcripts_loci" compare="sim_size" /> |
432 <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> | 445 <output file="gffcompare_out2.tracking" name="transcripts_tracking" /> |
433 <output file="gffcompare_out2.gtf" name="transcripts_combined" /> | 446 <output file="gffcompare_out2.gtf" name="transcripts_combined" /> |
434 </test> | 447 </test> |
435 | 448 |
436 <test expect_num_outputs="4"> | 449 <test expect_num_outputs="4"> |
447 </conditional> | 460 </conditional> |
448 <param name="use_seq_data" value="No" /> | 461 <param name="use_seq_data" value="No" /> |
449 <param name="discard_single_exon" value="" /> | 462 <param name="discard_single_exon" value="" /> |
450 <param name="max_dist_exon" value="100" /> | 463 <param name="max_dist_exon" value="100" /> |
451 <param name="max_dist_group" value="100" /> | 464 <param name="max_dist_group" value="100" /> |
452 <output file="gffcompare_out3.stats" name="transcripts_stats" lines_diff="6" /> | 465 <output file="gffcompare_out3.stats" name="transcripts_stats"/> |
453 <output file="gffcompare_out3.loci" name="transcripts_loci" /> | 466 <output file="gffcompare_out3.loci" name="transcripts_loci" compare="sim_size" /> |
454 <output file="gffcompare_out3.tracking" name="transcripts_tracking" /> | 467 <output file="gffcompare_out3.tracking" name="transcripts_tracking" /> |
455 <output file="gffcompare_out3.gtf" name="transcripts_annotated" /> | 468 <output file="gffcompare_out3.gtf" name="transcripts_annotated" /> |
456 </test> | 469 </test> |
457 </tests> | 470 </tests> |
458 <help> | 471 <help> |