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comparison gffcompare.xml @ 4:0f710191a66d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
author iuc
date Thu, 17 Oct 2019 03:01:26 -0400
parents 2bb86e2c417f
children f99dd58de04f
comparison
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3:2bb86e2c417f 4:0f710191a66d
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>