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GSNAP - add and refine param options for gmap v 2011-10-16
author Jim Johnson <jj@umn.edu>
date Tue, 08 Nov 2011 13:02:32 -0600
parents 52da588232b0
children
comparison
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3:72ab00e732c3 4:f49f5a460c74
38 #elif $refGenomeSource.use_snps.src == 'history': 38 #elif $refGenomeSource.use_snps.src == 'history':
39 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0: 39 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0:
40 -V $refGenomeSource.use_snps.snpindex.extra_files_path -v $refGenomeSource.use_snps.snpindex.metadata.snps_name 40 -V $refGenomeSource.use_snps.snpindex.extra_files_path -v $refGenomeSource.use_snps.snpindex.metadata.snps_name
41 #end if 41 #end if
42 #end if 42 #end if
43 #if $mode.__str__ != '': 43 #if $refGenomeSource.mode.__str__ != '':
44 --mode=$mode 44 --mode=$refGenomeSource.mode
45 #end if
46 #if $mapq_unique_score.__str__ != '':
47 --mapq-unique-score=$mapq_unique_score
45 #end if 48 #end if
46 #if $computation.options == "advanced": 49 #if $computation.options == "advanced":
47 #if $computation.max_mismatches.__str__ != '': 50 #if $computation.max_mismatches.__str__ != '':
48 --max-mismatches=$computation.max_mismatches 51 --max-mismatches=$computation.max_mismatches
49 #end if 52 #end if
73 #if $computation.suboptimal_levels.__str__ != '': 76 #if $computation.suboptimal_levels.__str__ != '':
74 --suboptimal-levels=$computation.suboptimal_levels 77 --suboptimal-levels=$computation.suboptimal_levels
75 #end if 78 #end if
76 #if $computation.adapter_strip.__str__ != '': 79 #if $computation.adapter_strip.__str__ != '':
77 --adapter-strip=$computation.adapter_strip 80 --adapter-strip=$computation.adapter_strip
81 #end if
82 #if $computation.trim_mismatch_score.__str__ != '':
83 --trim-mismatch-score=$computation.trim_mismatch_score
84 #end if
85 ## TODO - do we need these options (Is it tally XOR runlength?):
86 ## --tallydir= --use-tally=tally
87 ## --runlengthdir --use-runlength=runlength
88 #if $computation.use_tally != None and len($computation.use_tally.__str__) > 0:
89 ##--tallydir $os.path.dirname($computation.use_tally) --use-tally $os.path.basename($computation.use_tally)
90 --use-tally=$computation.use_tally
78 #end if 91 #end if
79 ## gmap options 92 ## gmap options
80 #if $computation.gmap_mode.__str__ != '' and $computation.gmap_mode.__str__ != 'None': 93 #if $computation.gmap_mode.__str__ != '' and $computation.gmap_mode.__str__ != 'None':
81 --gmap-mode='$computation.gmap_mode' 94 --gmap-mode='$computation.gmap_mode'
82 #end if 95 #end if
153 #if $result.creads_window_end.__str__ != '': 166 #if $result.creads_window_end.__str__ != '':
154 --creads-window-end=$result.creads_window_end 167 --creads-window-end=$result.creads_window_end
155 #end if 168 #end if
156 $result.creads_complement 169 $result.creads_complement
157 #end if 170 #end if
158 ## TODO - do we need these options (Is it tally XOR runlength?): 171 #if $results.split_output == 'yes':
159 ## --tallydir= --use-tally=tally 172 --split-output=gsnap_out
160 ## --runlengthdir --use-runlength=runlength 173 #if $results.fails.choice == 'nofails':
174 --nofails
175 #elif $results.fails.choice == 'failsonly':
176 --failsonly
177 #end if
178 $results.fails_as_input
179 #else
180 #if $results.fails.choice == 'nofails':
181 --nofails
182 #elif $results.fails.choice == 'failsonly':
183 --failsonly
184 $results.fails.fails_as_input
185 #end if
186 #end if
161 #if $seq.format == "gsnap_fasta": 187 #if $seq.format == "gsnap_fasta":
162 $seq.circularinput $seq.gsnap 188 $seq.circularinput $seq.gsnap
163 #else if $seq.format == "fastq": 189 #else if $seq.format == "fastq":
164 #if $seq.barcode_length.__str__ != '': 190 #if $seq.barcode_length.__str__ != '':
165 --barcode-length=$seq.barcode_length 191 --barcode-length=$seq.barcode_length
171 --fastq-id-end=$seq.fastq_id_end 197 --fastq-id-end=$seq.fastq_id_end
172 #end if 198 #end if
173 #if $seq.filter_chastity.__str__ != 'off': 199 #if $seq.filter_chastity.__str__ != 'off':
174 --filter-chastity=$seq.filter_chastity 200 --filter-chastity=$seq.filter_chastity
175 #end if 201 #end if
176 #if $seq.paired.ispaired.__str__ == "yes": 202 #if $seq.paired.ispaired.__str__ == 'yes':
177 #if $seq.paired.pairmax_dna.__str__ != '': 203 #if $seq.paired.pairmax_dna.__str__ != '':
178 --pairmax-dna=$seq.paired.pairmax_dna 204 --pairmax-dna=$seq.paired.pairmax_dna
179 #end if 205 #end if
180 #if $seq.paired.pairmax_rna.__str__ != '': 206 #if $seq.paired.pairmax_rna.__str__ != '':
181 --pairmax-rna=$seq.paired.pairmax_rna 207 --pairmax-rna=$seq.paired.pairmax_rna
183 $seq.fastq $seq.paired.fastq 209 $seq.fastq $seq.paired.fastq
184 #else 210 #else
185 $seq.fastq 211 $seq.fastq
186 #end if 212 #end if
187 #end if 213 #end if
188 #if $split_output == True 214 #if $results.split_output == 'yes':
189 2> $gsnap_stderr 215 2> $gsnap_stderr
190 #else 216 #else:
191 2> $gsnap_stderr > $results 217 #if $results.fails.choice.__str__ == 'failsonly' and $results.fails.fails_as_input.__str__ != '':
218 2> $gsnap_stderr > $gsnap_fq
219 #else
220 2> $gsnap_stderr > $gsnap_out
221 #end if
192 #end if 222 #end if
193 223
194 </command> 224 </command>
195 <inputs> 225 <inputs>
196 <!-- Input data --> 226 <!-- Input data -->
197 <conditional name="seq"> 227 <conditional name="seq">
198 <param name="format" type="select" label="&lt;H2&gt;Input Sequences&lt;/H2&gt;Select the input format" help=""> 228 <param name="format" type="select" label="&lt;H2&gt;Input Sequences&lt;/H2&gt;Select the input format" help="">
199 <option value="fastq">Fastq</option> 229 <option value="fastq">Fastq</option>
230 <!--
231 <option value="goby">Goby compact-reads</option>
232 -->
200 <option value="gsnap_fasta">GNSAP fasta</option> 233 <option value="gsnap_fasta">GNSAP fasta</option>
201 </param> 234 </param>
202 <when value="fastq"> 235 <when value="fastq">
203 <param name="fastq" type="data" format="fastq" label="Select a fastq dataset" /> 236 <param name="fastq" type="data" format="fastq" label="Select a fastq dataset" />
204 <conditional name="paired"> 237 <conditional name="paired">
205 <param name="ispaired" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Paired Reads"/> 238 <param name="ispaired" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use Paired Reads?"/>
206 <when value="no"/> 239 <when value="no"/>
207 <when value="yes"> 240 <when value="yes">
208 <param name="fastq" type="data" format="fastq" label="Select the paired reads reverse dataset" /> 241 <param name="fastq" type="data" format="fastq" label="Select the paired reads reverse dataset" />
209 <param name="orientation" type="select" label="Orientation of paired-end reads" help=""> 242 <param name="orientation" type="select" label="Orientation of paired-end reads" help="">
210 <option value="FR">fwd-rev, typical Illumina default</option> 243 <option value="FR">fwd-rev, typical Illumina default</option>
214 <param name="pairmax_dna" type="integer" value="" optional="true" label="Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000)." help="Used if no splice file is provided and novelsplicing is off."/> 247 <param name="pairmax_dna" type="integer" value="" optional="true" label="Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000)." help="Used if no splice file is provided and novelsplicing is off."/>
215 <param name="pairmax_rna" type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used novelspliceing is specified or a splice file is provided. Should probably match the value for localsplicedist."/> 248 <param name="pairmax_rna" type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used novelspliceing is specified or a splice file is provided. Should probably match the value for localsplicedist."/>
216 </when> 249 </when>
217 </conditional> 250 </conditional>
218 <param name="barcode_length" type="integer" value="" optional="true" label="Amount of barcode to remove from start of read (default 0)" /> 251 <param name="barcode_length" type="integer" value="" optional="true" label="Amount of barcode to remove from start of read (default 0)" />
219 <param name="fastq_id_start" type="integer" value="" optional="true" label="Starting field of identifier in FASTQ header, space-delimited, starting from 1" /> 252 <param name="fastq_id_start" type="integer" value="" optional="true" label="Starting field of identifier in FASTQ header, whitespace-delimited, starting from 1" />
220 <param name="fastq_id_end" type="integer" value="" optional="true" label="Ending field of identifier in FASTQ header, space-delimited, starting from 1" 253 <param name="fastq_id_end" type="integer" value="" optional="true" label="Ending field of identifier in FASTQ header, whitespace-delimited, starting from 1"
221 help="Examples: 254 help="Examples:
222 &lt;br&gt;@HWUSI-EAS100R:6:73:941:1973#0/1 255 &lt;br&gt;@HWUSI-EAS100R:6:73:941:1973#0/1
223 &lt;br&gt; . start=1, end=1 (default) => identifier is HWUSI-EAS100R:6:73:941:1973#0/1 256 &lt;br&gt; . start=1, end=1 (default) => identifier is HWUSI-EAS100R:6:73:941:1973#0/1
224 &lt;br&gt;@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36 257 &lt;br&gt;@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
225 &lt;br&gt; . start=1, end=1 => identifier is SRR001666.1 258 &lt;br&gt; . start=1, end=1 => identifier is SRR001666.1
236 <option value="off">off - no filtering</option> 269 <option value="off">off - no filtering</option>
237 <option value="either">either - a 'Y' on either end of a paired-end read</option> 270 <option value="either">either - a 'Y' on either end of a paired-end read</option>
238 <option value="both">both - a 'Y' is required on both ends of a paired-end read or the only end of a single-end read</option> 271 <option value="both">both - a 'Y' is required on both ends of a paired-end read or the only end of a single-end read</option>
239 </param> 272 </param>
240 </when> 273 </when>
274 <!--
275 <when value="goby">
276 </when>
277 -->
241 <when value="gsnap_fasta"> 278 <when value="gsnap_fasta">
242 <param name="gsnap" type="data" format="fasta" label="Select a single-end dataset" help="GSNAP fasta must have the sequence entirely on one line, a second line is interpreted as the paired-end sequence"/> 279 <param name="gsnap" type="data" format="fasta" label="Select a single-end dataset" help="GSNAP fasta must have the sequence entirely on one line, a second line is interpreted as the paired-end sequence"/>
243 <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/> 280 <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/>
244 </when> 281 </when>
282
245 </conditional> 283 </conditional>
246 284 <param name="mapq_unique_score" type="integer" value="" optional="true" label="MAPQ score threshold"
247 <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase."> 285 help="For multiple results, consider as a unique result if only one of the results has a MAPQ score equal or greater than this
248 <option value="">standard</option> 286 (if not selected, then reports all multiple results, up to npaths)" />
249 <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
250 <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
251 <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option>
252 <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option>
253 </param>
254 287
255 <!-- GMAPDB for alignment --> 288 <!-- GMAPDB for alignment -->
256 <conditional name="refGenomeSource"> 289 <conditional name="refGenomeSource">
257 <param name="genomeSource" type="select" label="&lt;HR&gt;&lt;H2&gt;Align To&lt;/H2&gt;Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 290 <param name="genomeSource" type="select" label="&lt;HR&gt;&lt;H2&gt;Align To&lt;/H2&gt;Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
258 <option value="indexed">Use a built-in index</option> 291 <option value="indexed">Use a built-in index</option>
280 <filter type="add_value" name="" value=""/> 313 <filter type="add_value" name="" value=""/>
281 <filter type="sort_by" column="3"/> 314 <filter type="sort_by" column="3"/>
282 </options> 315 </options>
283 </param> 316 </param>
284 317
318 <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase.">
319 <option value="">standard</option>
320 <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
321 <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
322 <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option>
323 <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option>
324 </param>
325
285 <conditional name="use_splicing"> 326 <conditional name="use_splicing">
286 <param name="src" type="select" label="Known Splicesite and Introns" 327 <param name="src" type="select" label="&lt;HR&gt;Known Splicesite and Introns"
287 help="Look for splicing involving known sites or known introns at short or long distances 328 help="Look for splicing involving known sites or known introns at short or long distances
288 See README instructions for the distinction between known sites and known introns"> 329 See README instructions for the distinction between known sites and known introns">
289 <option value="none" selected="true">None</option> 330 <option value="none" selected="true">None</option>
290 <option value="gmapdb">From the GMAP Database</option> 331 <option value="gmapdb">From the GMAP Database</option>
291 <option value="history">A Map in your history</option> 332 <option value="history">A Map in your history</option>
308 </param> 349 </param>
309 </when> 350 </when>
310 </conditional> 351 </conditional>
311 352
312 <conditional name="use_snps"> 353 <conditional name="use_snps">
313 <param name="src" type="select" label="Known SNPs" help="for SNP tolerant alignments"> 354 <param name="src" type="select" label="&lt;HR&gt;Known SNPs" help="for SNP tolerant alignments">
314 <option value="none" selected="true">None</option> 355 <option value="none" selected="true">None</option>
315 <option value="gmapdb">From the GMAP Database</option> 356 <option value="gmapdb">From the GMAP Database</option>
316 <option value="history">A SNP Index in your history</option> 357 <option value="history">A SNP Index in your history</option>
317 </param> 358 </param>
318 <when value="none"/> 359 <when value="none"/>
342 <options> 383 <options>
343 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/> 384 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/>
344 </options> 385 </options>
345 </param> 386 </param>
346 387
388 <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase.">
389 <option value="">standard</option>
390 <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
391 <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
392 <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option>
393 <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option>
394 </param>
395
347 <conditional name="use_splicing"> 396 <conditional name="use_splicing">
348 <param name="src" type="select" label="Known Splicesite and Introns" 397 <param name="src" type="select" label="&lt;HR&gt;Known Splicesite and Introns"
349 help="Look for splicing involving known sites or known introns at short or long distances 398 help="Look for splicing involving known sites or known introns at short or long distances
350 See README instructions for the distinction between known sites and known introns"> 399 See README instructions for the distinction between known sites and known introns">
351 <option value="none" selected="true">None</option> 400 <option value="none" selected="true">None</option>
352 <option value="gmapdb">From the GMAP Database</option> 401 <option value="gmapdb">From the GMAP Database</option>
353 <option value="history">A Map in your history</option> 402 <option value="history">A Map in your history</option>
365 </param> 414 </param>
366 </when> 415 </when>
367 </conditional> 416 </conditional>
368 417
369 <conditional name="use_snps"> 418 <conditional name="use_snps">
370 <param name="src" type="select" label="Known SNPs" help="for SNP tolerant alignments"> 419 <param name="src" type="select" label="&lt;HR&gt;Known SNPs" help="for SNP tolerant alignments">
371 <option value="none" selected="true">None</option> 420 <option value="none" selected="true">None</option>
372 <option value="gmapdb">From the GMAP Database</option> 421 <option value="gmapdb">From the GMAP Database</option>
373 <option value="history">A SNP Index in your history</option> 422 <option value="history">A SNP Index in your history</option>
374 </param> 423 </param>
375 <when value="none"/> 424 <when value="none"/>
424 <option value="paired" selected="true">paired</option> 473 <option value="paired" selected="true">paired</option>
425 <option value="off">off</option> 474 <option value="off">off</option>
426 </param> 475 </param>
427 <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)" 476 <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)"
428 help="to turn off trimming, specify 0"/> 477 help="to turn off trimming, specify 0"/>
478 <param name="use_tally" type="data" format="tally.iit" optional="true" metadata_name="dbkey" label="Select a tally IIT file to resolve concordant multiple results"
479 help="generated by gsnap_tally and iit_store"/>
480
481 <!--
482 tallydir=STRING Directory for tally IIT file to resolve concordant multiple results (default is
483 location of genome index files specified using -D and -d). Note: can
484 just give full path name to use-tally instead.
485 use-tally=STRING Use this tally IIT file to resolve concordant multiple results
486 runlengthdir=STRING Directory for runlength IIT file to resolve concordant multiple results (default is
487 location of genome index files specified using -D and -d). Note: can
488 just give full path name to use-runlength instead.
489 use-runlength=STRING Use this runlength IIT file to resolve concordant multiple results
490 -->
429 491
430 <!-- Options for GMAP alignment within GSNAP --> 492 <!-- Options for GMAP alignment within GSNAP -->
431 <param name="gmap_mode" type="select" multiple="true" optional="true" label="Cases to use GMAP for complex alignments containing multiple splices or indels" help=""> 493 <param name="gmap_mode" type="select" multiple="true" optional="true" display="checkboxes" label="Cases to use GMAP for complex alignments containing multiple splices or indels"
432 <option value="pairsearch">pairsearch</option> 494 help="Default: pairsearch,terminal,improve">
433 <option value="terminal">terminal</option> 495 <option value="pairsearch" selected="true">pairsearch</option>
434 <option value="improve">improve</option> 496 <option value="terminal" selected="true">terminal</option>
497 <option value="improve" selected="true">improve</option>
435 </param> 498 </param>
436 <param name="trigger_score_for_gmap" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 5)" 499 <param name="trigger_score_for_gmap" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 5)"
437 help="Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5)" /> 500 help="Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5)" />
438 <param name="max_gmap_pairsearch" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 3)" 501 <param name="max_gmap_pairsearch" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 3)"
439 help="Perform GMAP pairsearch on nearby genomic regions up to this many candidate ends (default 3)." /> 502 help="Perform GMAP pairsearch on nearby genomic regions up to this many candidate ends (default 3)." />
454 <option value="advanced">Set Splicing Options</option> 517 <option value="advanced">Set Splicing Options</option>
455 </param> 518 </param>
456 <when value="default"/> 519 <when value="default"/>
457 <when value="advanced"> 520 <when value="advanced">
458 <!-- Splicing options for RNA-Seq --> 521 <!-- Splicing options for RNA-Seq -->
459 <!-- use-splices This should be either a select list from the gmapdb maps or a data type using splicesdir and use-splices --> 522 <!-- use-splicing This should be either a select list from the gmapdb maps or a data type using splicesdir and use-splicing -->
460 <!-- Neither novel splicing (-N) nor known splicing (-s) turned on => assume reads are DNA-Seq (genomic) --> 523 <!-- Neither novel splicing (-N) nor known splicing (-s) turned on => assume reads are DNA-Seq (genomic) -->
461 <param name="novelsplicing" type="boolean" checked="false" truevalue="--novelsplicing=1" falsevalue="" label="Look for novel splicing "/> 524 <param name="novelsplicing" type="boolean" checked="false" truevalue="--novelsplicing=1" falsevalue="" label="Look for novel splicing "/>
462 <param name="localsplicedist" type="integer" value="" optional="true" label="Definition of local novel splicing event (default 200000)"/> 525 <param name="localsplicedist" type="integer" value="" optional="true" label="Definition of local novel splicing event (default 200000)"/>
463 <param name="local_splice_penalty" type="integer" value="" optional="true" label="Penalty for a local splice (default 0). Counts against mismatches allowed"/> 526 <param name="local_splice_penalty" type="integer" value="" optional="true" label="Penalty for a local splice (default 0). Counts against mismatches allowed"/>
464 <param name="distant_splice_penalty" type="integer" value="" optional="true" label="Penalty for a distant splice (default 3). Counts against mismatches allowed"/> 527 <param name="distant_splice_penalty" type="integer" value="" optional="true" label="Penalty for a distant splice (default 3). Counts against mismatches allowed"
465 <param name="local_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for local spliced alignments (default 15, min is 14)"/> 528 help="A distant splice is one where the intron length exceeds the value of localsplicedist or is an
466 <param name="distant_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for distant spliced alignments (default 16, min is 14)"/> 529 inversion, scramble, or translocation between two different chromosomes. Counts against mismatches allowed"/>
467 <param name="shortend_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for distant spliced alignments (default 16, min is 14)"/> 530 <param name="distant_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for distant spliced alignments"
531 help="(default 16, min is the kmer length)"/>
532 <param name="shortend_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for short-end spliced alignments"
533 help="(default 2, but unless known splice sites are provided, GSNAP may still need the end length to be the value of kmer size to find a given splice"/>
468 <param name="distant_splice_identity" type="float" value="" optional="true" label="Minimum identity at end required for distant spliced alignments (default 0.95)"/> 534 <param name="distant_splice_identity" type="float" value="" optional="true" label="Minimum identity at end required for distant spliced alignments (default 0.95)"/>
535 <param name="antistranded_penalty" type="integer" value="" optional="true" label="Penalty for antistranded splicing when using stranded RNA-Seq protocols"
536 help="A positive value, such as 1, expects antisense on the first read and sense on the second read.
537 Default is 0, which treats sense and antisense equally well"/>
469 </when> 538 </when>
470 </conditional> 539 </conditional>
471 540
472 <!-- Output data --> 541 <!-- Output data -->
473 <conditional name="output"> 542 <conditional name="output">
487 </when> 556 </when>
488 </conditional> 557 </conditional>
489 <conditional name="result"> 558 <conditional name="result">
490 <param name="format" type="select" label="Select the output format" help=""> 559 <param name="format" type="select" label="Select the output format" help="">
491 <option value="sam">SAM</option> 560 <option value="sam">SAM</option>
561 <!-- goby should only be an option if the input is in goby format
492 <option value="goby">Goby</option> 562 <option value="goby">Goby</option>
563 -->
493 <option value="gsnap">GSNAP default output</option> 564 <option value="gsnap">GSNAP default output</option>
494 </param> 565 </param>
495 <when value="gsnap"/> 566 <when value="gsnap">
567 </when>
496 <when value="sam"> 568 <when value="sam">
497 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/> 569 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/>
498 <param name="read_group_id" type="text" value="" optional="true" label="Value to put into read-group id (RG-ID) field"/> 570 <param name="read_group_id" type="text" value="" optional="true" label="Value to put into read-group id (RG-ID) field"/>
499 <param name="read_group_name" type="text" value="" optional="true" label="Value to put into read-group name (RG-SM) field"/> 571 <param name="read_group_name" type="text" value="" optional="true" label="Value to put into read-group name (RG-SM) field"/>
500 <param name="read_group_library" type="text" value="" optional="true" label="Value to put into read-group library (RG-LB) field"/> 572 <param name="read_group_library" type="text" value="" optional="true" label="Value to put into read-group library (RG-LB) field"/>
501 <param name="read_group_platform" type="text" value="" optional="true" label="Value to put into read-group library platform (RG-PL) field"/> 573 <param name="read_group_platform" type="text" value="" optional="true" label="Value to put into read-group library platform (RG-PL) field"/>
502 <param name="quality_shift" type="integer" value="" optional="true" label="Shift FASTQ quality scores by this amount in SAM output (default -31)"/> 574 <param name="quality_shift" type="integer" value="" optional="true" label="Shift FASTQ quality scores by this amount in SAM output (default -31)"/>
503 </when> 575 </when>
576 <!--
504 <when value="goby"> 577 <when value="goby">
505 <param name="goby_output" type="text" value="" label="Basename for Goby output files"/> 578 <param name="goby_output" type="text" value="" label="Basename for Goby output files"/>
506 <param name="creads_window_start" type="integer" value="" optional="true" label="Compact reads window start (default: 0=start of file)"/> 579 <param name="creads_window_start" type="integer" value="" optional="true" label="Compact reads window start (default: 0=start of file)"/>
507 <param name="creads_window_end" type="integer" value="" optional="true" label="Compact reads window end (default: 0=end of file)"/> 580 <param name="creads_window_end" type="integer" value="" optional="true" label="Compact reads window end (default: 0=end of file)"/>
508 <param name="creads_complement" type="boolean" truevalue="--creads-complement" falsevalue="" checked="false" label="Complement read sequences (without reversing)"/> 581 <param name="creads_complement" type="boolean" truevalue="-\-creads-complement" falsevalue="" checked="false" label="Complement read sequences (without reversing)"/>
509 </when> 582 </when>
583 -->
510 </conditional> 584 </conditional>
511 <param name="split_output" type="boolean" truevalue="--split-output=gsnap_out" falsevalue="" checked="false" label="Separate outputs" 585 <!-- TODO combine fails and split_output -->
512 help="Separate outputs for: nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult results"/> 586
587 <conditional name="results">
588 <param name="split_output" type="select" label="&lt;HR&gt;Split outputs"
589 help="Separate outputs for: nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult results">
590 <option value="no">no</option>
591 <option value="yes">yes</option>
592 </param>
593 <when value="no">
594 <conditional name="fails">
595 <param name="choice" type="select" label="How to deal with fails" help="">
596 <option value="default">default - include them in results</option>
597 <option value="nofails">nofails - exclude fails from results</option>
598 <option value="failsonly">failsonly - only output failing results</option>
599 </param>
600 <when value="default"/>
601 <when value="nofails"/>
602 <when value="failsonly">
603 <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format"
604 help=""/>
605 </when>
606 </conditional>
607 </when>
608 <when value="yes">
609 <conditional name="fails">
610 <param name="choice" type="select" label="How to deal with fails" help="">
611 <option value="default">default - include them in results</option>
612 <option value="nofails">nofails - exclude fails from results</option>
613 <option value="failsonly">failsonly - only output failing results</option>
614 </param>
615 <when value="default"/>
616 <when value="nofails"/>
617 <when value="failsonly"/>
618 </conditional>
619 <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format"
620 help=""/>
621 </when>
622 </conditional>
623
513 </inputs> 624 </inputs>
514 <outputs> 625 <outputs>
515 <data format="txt" name="gsnap_stderr" label="${tool.name} on ${on_string}: stderr"/> 626 <data format="txt" name="gsnap_stderr" label="${tool.name} on ${on_string}: gsnap.log"/>
516 <data format="txt" name="results" label="${tool.name} on ${on_string} ${result.format}" > 627
517 <filter>(split_output == False)</filter> 628 <data format="txt" name="gsnap_out" label="${tool.name} on ${on_string} ${result.format}" >
518 <change_format> 629 <filter>(results['split_output'] == 'no' and (results['fails']['choice'] != 'failsonly' or results['fails']['fails_as_input'] == False))</filter>
519 <when input="result['format']" value="sam" format="sam"/> 630 <change_format>
520 </change_format> 631 <when input="result['format']" value="sam" format="sam"/>
521 </data> 632 <when input="result['format']" value="gsnap" format="gsnap"/>
633 </change_format>
634 </data>
635
636 <data format="fastq" name="gsnap_fq" label="${tool.name} on ${on_string} fails.fq" >
637 <filter>(results['split_output'] == 'no' and results['fails']['choice'] == 'failsonly' and results['fails']['fails_as_input'] == True)</filter>
638 </data>
639
522 <!-- nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, concordant_mult --> 640 <!-- nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, concordant_mult -->
523 <data format="txt" name="concordant_mult" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.concordant_mult"> 641
524 <filter>(split_output == True)</filter> 642 <data format="txt" name="unpaired_mult" label="${tool.name} on ${on_string} unpaired_mult.${result.format}" from_work_dir="gsnap_out.unpaired_mult">
525 <change_format> 643 <filter>(results['split_output'] == 'yes')</filter>
526 <when input="result['format']" value="sam" format="sam"/> 644 <change_format>
527 </change_format> 645 <when input="result['format']" value="sam" format="sam"/>
528 </data> 646 <when input="result['format']" value="gsnap" format="gsnap"/>
529 <data format="txt" name="concordant_uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.concordant_uniq"> 647 </change_format>
530 <filter>(split_output == True)</filter> 648 </data>
531 <change_format> 649 <data format="txt" name="unpaired_uniq" label="${tool.name} on ${on_string} unpaired_uniq.${result.format}" from_work_dir="gsnap_out.unpaired_uniq">
532 <when input="result['format']" value="sam" format="sam"/> 650 <filter>(results['split_output'] == 'yes')</filter>
533 </change_format> 651 <change_format>
534 </data> 652 <when input="result['format']" value="sam" format="sam"/>
535 <data format="txt" name="paired_mult" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.paired_mult"> 653 <when input="result['format']" value="gsnap" format="gsnap"/>
536 <filter>(split_output == True)</filter> 654 </change_format>
537 <change_format> 655 </data>
538 <when input="result['format']" value="sam" format="sam"/> 656 <data format="txt" name="unpaired_transloc" label="${tool.name} on ${on_string} unpaired_transloc.${result.format}" from_work_dir="gsnap_out.unpaired_transloc">
539 </change_format> 657 <filter>(results['split_output'] == 'yes')</filter>
540 </data> 658 <change_format>
541 <data format="txt" name="paired_uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.paired_uniq"> 659 <when input="result['format']" value="sam" format="sam"/>
542 <filter>(split_output == True)</filter> 660 <when input="result['format']" value="gsnap" format="gsnap"/>
543 <change_format> 661 </change_format>
544 <when input="result['format']" value="sam" format="sam"/> 662 </data>
545 </change_format> 663 <data format="txt" name="halfmapping_mult" label="${tool.name} on ${on_string} halfmapping_mult.${result.format}" from_work_dir="gsnap_out.halfmapping_mult">
546 </data> 664 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
547 <data format="txt" name="unpaired_mult" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.unpaired_mult"> 665 <change_format>
548 <filter>(split_output == True)</filter> 666 <when input="result['format']" value="sam" format="sam"/>
549 <change_format> 667 <when input="result['format']" value="gsnap" format="gsnap"/>
550 <when input="result['format']" value="sam" format="sam"/> 668 </change_format>
551 </change_format> 669 </data>
552 </data> 670 <data format="txt" name="halfmapping_uniq" label="${tool.name} on ${on_string} halfmapping_uniq.${result.format}" from_work_dir="gsnap_out.halfmapping_uniq">
553 <data format="txt" name="unpaired_uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.unpaired_uniq"> 671 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
554 <filter>(split_output == True)</filter> 672 <change_format>
555 <change_format> 673 <when input="result['format']" value="sam" format="sam"/>
556 <when input="result['format']" value="sam" format="sam"/> 674 <when input="result['format']" value="gsnap" format="gsnap"/>
557 </change_format> 675 </change_format>
558 </data> 676 </data>
559 <data format="txt" name="halfmapping_mult" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.halfmapping_mult"> 677 <data format="txt" name="halfmapping_transloc" label="${tool.name} on ${on_string} halfmapping_transloc.${result.format}" from_work_dir="gsnap_out.halfmapping_transloc">
560 <filter>(split_output == True)</filter> 678 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
561 <change_format> 679 <change_format>
562 <when input="result['format']" value="sam" format="sam"/> 680 <when input="result['format']" value="sam" format="sam"/>
563 </change_format> 681 <when input="result['format']" value="gsnap" format="gsnap"/>
564 </data> 682 </change_format>
565 <data format="txt" name="halfmapping_uniq" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.halfmapping_uniq"> 683 </data>
566 <filter>(split_output == True)</filter> 684 <data format="txt" name="paired_mult" label="${tool.name} on ${on_string} paired_mult.${result.format}" from_work_dir="gsnap_out.paired_mult">
567 <change_format> 685 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
568 <when input="result['format']" value="sam" format="sam"/> 686 <change_format>
569 </change_format> 687 <when input="result['format']" value="sam" format="sam"/>
570 </data> 688 <when input="result['format']" value="gsnap" format="gsnap"/>
571 <data format="txt" name="nomapping" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.nomapping"> 689 </change_format>
572 <filter>(split_output == True)</filter> 690 </data>
573 <change_format> 691 <data format="txt" name="paired_uniq" label="${tool.name} on ${on_string} paired_uniq.${result.format}" from_work_dir="gsnap_out.paired_uniq">
574 <when input="result['format']" value="sam" format="sam"/> 692 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
575 </change_format> 693 <change_format>
576 </data> 694 <when input="result['format']" value="sam" format="sam"/>
695 <when input="result['format']" value="gsnap" format="gsnap"/>
696 </change_format>
697 </data>
698 <data format="txt" name="paired_transloc" label="${tool.name} on ${on_string} paired_transloc.${result.format}" from_work_dir="gsnap_out.paired_transloc">
699 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
700 <change_format>
701 <when input="result['format']" value="sam" format="sam"/>
702 <when input="result['format']" value="gsnap" format="gsnap"/>
703 </change_format>
704 </data>
705
706 <data format="txt" name="concordant_mult" label="${tool.name} on ${on_string} concordant_mult.${result.format}" from_work_dir="gsnap_out.concordant_mult">
707 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
708 <change_format>
709 <when input="result['format']" value="sam" format="sam"/>
710 <when input="result['format']" value="gsnap" format="gsnap"/>
711 </change_format>
712 </data>
713 <data format="txt" name="concordant_uniq" label="${tool.name} on ${on_string} concordant_uniq.${result.format}" from_work_dir="gsnap_out.concordant_uniq">
714 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
715 <change_format>
716 <when input="result['format']" value="sam" format="sam"/>
717 <when input="result['format']" value="gsnap" format="gsnap"/>
718 </change_format>
719 </data>
720 <data format="txt" name="concordant_transloc" label="${tool.name} on ${on_string} concordant_transloc.${result.format}" from_work_dir="gsnap_out.concordant_transloc">
721 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
722 <change_format>
723 <when input="result['format']" value="sam" format="sam"/>
724 <when input="result['format']" value="gsnap" format="gsnap"/>
725 </change_format>
726 </data>
727
728 <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gsnap_out.nomapping">
729 <filter>(results['split_output'] == 'yes' and results['fails_as_input'] == False)</filter>
730 <change_format>
731 <when input="result['format']" value="sam" format="sam"/>
732 <when input="result['format']" value="gsnap" format="gsnap"/>
733 </change_format>
734 </data>
735
736 <data format="fastq" name="nomapping_fq" label="${tool.name} on ${on_string} nomapping.fq" from_work_dir="gsnap_out.nomapping.fq">
737 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == False)</filter>
738 </data>
739
740 <data format="fastq" name="nomapping_1_fq" label="${tool.name} on ${on_string} nomapping.1.fq" from_work_dir="gsnap_out.nomapping.1.fq">
741 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
742 </data>
743
744 <data format="fastq" name="nomapping_2_fq" label="${tool.name} on ${on_string} nomapping.2.fq" from_work_dir="gsnap_out.nomapping.2.fq">
745 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
746 </data>
747
748 <!-- Will problay need wrapper code to generate composite datatype for goby alignment
749 <data format="gobyalignment" name="goby_alignment" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.nomapping">
750 <filter>result['format'] == 'goby'</filter>
751 </data>
752 -->
577 753
578 </outputs> 754 </outputs>
579 <tests> 755 <tests>
580 </tests> 756 </tests>
581 757