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comparison flexbar.xml @ 41:b0847c1e320b draft

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Uploaded
author jtilman
date Tue, 03 Jul 2018 07:36:49 -0400
parents ae7d2b47ad07
children afaa5daf84ac
comparison
equal deleted inserted replaced
40:2fcee21876db 41:b0847c1e320b
16 <command detect_errors="aggressive"> 16 <command detect_errors="aggressive">
17 17
18 <![CDATA[ 18 <![CDATA[
19 19
20 #if $reads.mode == "se": 20 #if $reads.mode == "se":
21 ln -s '$reads.rs' '$rsout'_input.'$reads.rs.extension' && 21 ln -s '$reads.rs' '$outlog'_input1.'$reads.rs.extension' &&
22 #elif $reads.mode == "pe": 22 #elif $reads.mode == "pe":
23 ln -s '$reads.r1' '$r1out'_input.'$reads.r1.extension' && 23 ln -s '$reads.r1' '$outlog'_input1.'$reads.r1.extension' &&
24 ln -s '$reads.r2' '$r2out'_input.'$reads.r2.extension' && 24 ln -s '$reads.r2' '$outlog'_input2.'$reads.r2.extension' &&
25 #else: 25 #else:
26 ln -s '$reads.rc.forward' '$rcout.forward'_input.'$reads.rc.forward.extension' && 26 ln -s '$reads.rc.forward' '$outlog'_input1.'$reads.rc.forward.extension' &&
27 ln -s '$reads.rc.reverse' '$rcout.reverse'_input.'$reads.rc.reverse.extension' && 27 ln -s '$reads.rc.reverse' '$outlog'_input2.'$reads.rc.reverse.extension' &&
28 #end if 28 #end if
29
30 #if $cBarcodes.select == "on":
31
32 mkdir flexbar_barcoded &&
33
34 #if $cBarcodes.bAdvanced.cbReads.select == "yes":
35 ln -s '$cBarcodes.bAdvanced.cbReads.bReads' '$outlog'_input3.'$cBarcodes.bAdvanced.cbReads.bReads.extension' &&
36 #end if
37 #end if
38
29 39
30 '$__tool_directory__/flexbar.pl' flexbar 40 '$__tool_directory__/flexbar.pl' flexbar
31 41
32 --threads \${GALAXY_SLOTS:-1} 42 --threads \${GALAXY_SLOTS:-1}
33 43
34 #if $reads.mode == "se": 44 #if $reads.mode == "se":
35 --reads '$rsout'_input.'$reads.rs.extension' 45 --reads '$outlog'_input1.'$reads.rs.extension'
36 #elif $reads.mode == "pe": 46 #elif $reads.mode == "pe":
37 --reads '$r1out'_input.'$reads.r1.extension' 47 --reads '$outlog'_input1.'$reads.r1.extension'
38 --reads2 '$r2out'_input.'$reads.r2.extension' 48 --reads2 '$outlog'_input2.'$reads.r2.extension'
39 #else: 49 #else:
40 --reads '$rcout.forward'_input.'$reads.rc.forward.extension' 50 --reads '$outlog'_input1.'$reads.rc.forward.extension'
41 --reads2 '$rcout.reverse'_input.'$reads.rc.reverse.extension' 51 --reads2 '$outlog'_input2.'$reads.rc.reverse.extension'
42 #end if 52 #end if
43 53
44 --max-uncalled $maxUncalled 54 --max-uncalled $maxUncalled
45 --min-read-length $minReadLen 55 --min-read-length $minReadLen
46 56
97 #end if 107 #end if
98 #if $cTrimQual.select == "bwa": 108 #if $cTrimQual.select == "bwa":
99 --qtrim BWA 109 --qtrim BWA
100 --qtrim-threshold $cTrimQual.trimQualBWA 110 --qtrim-threshold $cTrimQual.trimQualBWA
101 $cTrimQual.trimQualPostBWA 111 $cTrimQual.trimQualPostBWA
112 #end if
113
114
115 #if $cBarcodes.select == "on":
116
117 --target flexbar_barcoded/flexbarOut
118
119 #if $cBarcodes.ccBarcodes.select == "file":
120 --barcodes $cBarcodes.ccBarcodes.barcodeFile
121 #end if
122 #if $cBarcodes.ccBarcodes.select == "files":
123 --barcodes $cBarcodes.ccBarcodes.barcodeFile1
124 --barcodes2 $cBarcodes.ccBarcodes.barcodeFile2
125 #end if
126
127 --barcode-error-rate $cBarcodes.bThresh
128
129 --barcode-trim-end $cBarcodes.bTrimEnd
130
131 #if $cBarcodes.bAdvanced.cbReads.select == "yes":
132 --barcode-reads '$outlog'_input3.'$cBarcodes.bAdvanced.cbReads.bReads.extension'
133 #end if
134
135 #if $cBarcodes.bAdvanced.cbMinOverlap.select == "yes":
136 --barcode-min-overlap $cBarcodes.bAdvanced.cbMinOverlap.bMinOverlap
137 #end if
138
139 $cBarcodes.bAdvanced.bKeep
140 $cBarcodes.bAdvanced.bUnassigned
141
142 #if $cBarcodes.bAdvanced.cbTailLen.select == "yes":
143 --barcode-tail-length $cBarcodes.bAdvanced.cbTailLen.bTailLen
144 #end if
145
146 #if $cBarcodes.bAdvanced.cbAlignScores.select == "yes":
147 --barcode-match $cBarcodes.bAdvanced.cbAlignScores.bMatch
148 --barcode-mismatch $cBarcodes.bAdvanced.cbAlignScores.bMismatch
149 --barcode-gap $cBarcodes.bAdvanced.cbAlignScores.bGap
150 #end if
102 #end if 151 #end if
103 152
104 153
105 #if $cAdapters.select == "on": 154 #if $cAdapters.select == "on":
106 155
194 --bundles $cAddOptions.cReadBundle.bundles 243 --bundles $cAddOptions.cReadBundle.bundles
195 #end if 244 #end if
196 #end if 245 #end if
197 #end if 246 #end if
198 247
199 248 #if $cBarcodes.select == "off":
200 #if $reads.mode == "se": 249 #if $reads.mode == "se":
201 --output-reads '$rsout'.'$reads.rs.extension' 250 --output-reads '$rsout'.'$reads.rs.extension'
202 #elif $reads.mode == "pe": 251 #elif $reads.mode == "pe":
203 --output-reads '$r1out'.'$reads.r1.extension' 252 --output-reads '$r1out'.'$reads.r1.extension'
204 --output-reads2 '$r2out'.'$reads.r2.extension' 253 --output-reads2 '$r2out'.'$reads.r2.extension'
205 #else: 254 #else:
206 --output-reads '$rcout.forward'.'$reads.rc.forward.extension' 255 --output-reads '$rcout.forward'.'$reads.rc.forward.extension'
207 --output-reads2 '$rcout.reverse'.'$reads.rc.reverse.extension' 256 --output-reads2 '$rcout.reverse'.'$reads.rc.reverse.extension'
257 #end if
208 #end if 258 #end if
209 259
210 --output-log '$outlog' 260 --output-log '$outlog'
261
262 #if $cBarcodes.select == "on":
263 flexbar_barcoded
264 #end if
211 265
212 ]]> 266 ]]>
213 </command> 267 </command>
214 268
215 269
283 </param> 337 </param>
284 </when> 338 </when>
285 </conditional> 339 </conditional>
286 340
287 341
342 <conditional name="cBarcodes">
343 <param name="select" type="select" label="4) Barcode detection">
344 <option value="off" selected="true">Off</option>
345 <option value="on">On</option>
346 </param>
347 <when value="off">
348 </when>
349 <when value="on">
350 <conditional name="ccBarcodes">
351 <param name="select" type="select" label="Barcodes">
352 <option value="file" selected="true">Barcode file</option>
353 <option value="files">Two barcode files</option>
354 </param>
355 <when value="file">
356 <param format="fasta" name="barcodeFile" type="data" label="Fasta file with barcodes for reads 1"/>
357 </when>
358 <when value="files">
359 <param format="fasta" name="barcodeFile1" type="data" label="Fasta file with barcodes for reads 1"/>
360 <param format="fasta" name="barcodeFile2" type="data" label="Fasta file with barcodes for reads 2"/>
361 </when>
362 </conditional>
363
364 <param name="bThresh" size="4" type="float" value="0.0" label="Error rate" help="allowed fraction of mismatches and indels"/>
365
366 <param name="bTrimEnd" type="select" label="Trim-end mode">
367 <option value="LTAIL" selected="true">Left tail</option>
368 <option value="LEFT">Left</option>
369 <option value="RTAIL">Right tail</option>
370 <option value="RIGHT">Right</option>
371 <option value="ANY">Any</option>
372 </param>
373
374 <section name="bAdvanced" title="Advanced options" expanded="false">
375
376 <conditional name="cbReads">
377 <param name="select" type="select" label="Separate barcode reads">
378 <option value="no" selected="true">No</option>
379 <option value="yes">Yes</option>
380 </param>
381 <when value="no">
382 </when>
383 <when value="yes">
384 <param name="bReads" type="data" label="Fastq file with separate barcode reads" format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz,fastqsanger.bz2,fastqsolexa.bz2,fastqillumina.bz2"/>
385 </when>
386 </conditional>
387
388 <conditional name="cbMinOverlap">
389 <param name="select" type="select" label="Change minimum overlap" help="default: barcode length">
390 <option value="no" selected="true">No</option>
391 <option value="yes">Yes</option>
392 </param>
393 <when value="no">
394 </when>
395 <when value="yes">
396 <param name="bMinOverlap" size="4" type="integer" value="" label="Minimum overlap"/>
397 </when>
398 </conditional>
399
400 <param name="bKeep" type="select" label="Remove barcodes within reads">
401 <option value="" selected="true">Yes</option>
402 <option value="--barcode-keep">No</option>
403 </param>
404
405 <param name="bUnassigned" type="select" label="Include unassigned reads">
406 <option value="" selected="true">No</option>
407 <option value="--barcode-unassigned">Yes</option>
408 </param>
409
410 <conditional name="cbTailLen">
411 <param name="select" type="select" label="Change tail length">
412 <option value="no" selected="true">No</option>
413 <option value="yes">Yes</option>
414 </param>
415 <when value="no">
416 </when>
417 <when value="yes">
418 <param name="bTailLen" size="4" type="integer" value="" label="Tail length"/>
419 </when>
420 </conditional>
421
422 <conditional name="cbAlignScores">
423 <param name="select" type="select" label="Modify alignment scores">
424 <option value="no" selected="true">No</option>
425 <option value="yes">Yes</option>
426 </param>
427 <when value="no">
428 </when>
429 <when value="yes">
430 <param name="bMatch" size="3" type="integer" value="1" label="Match"/>
431 <param name="bMismatch" size="3" type="integer" value="-1" label="Mismatch"/>
432 <param name="bGap" size="3" type="integer" value="-9" label="Gap"/>
433 </when>
434 </conditional>
435 </section>
436 </when>
437 </conditional>
438
439
288 <conditional name="cAdapters"> 440 <conditional name="cAdapters">
289 <param name="select" type="select" label="4) Adapter removal"> 441 <param name="select" type="select" label="5) Adapter removal">
290 <option value="off" selected="true">Off</option> 442 <option value="off" selected="true">Off</option>
291 <option value="on">On</option> 443 <option value="on">On</option>
292 </param> 444 </param>
293 <when value="off"> 445 <when value="off">
294 </when> 446 </when>
409 </when> 561 </when>
410 </conditional> 562 </conditional>
411 563
412 564
413 <conditional name="hTrim"> 565 <conditional name="hTrim">
414 <param name="select" type="select" label="5) Trimming of homopolymers"> 566 <param name="select" type="select" label="6) Trimming of homopolymers">
415 <option value="off" selected="true">Off</option> 567 <option value="off" selected="true">Off</option>
416 <option value="on">On</option> 568 <option value="on">On</option>
417 </param> 569 </param>
418 <when value="off"> 570 <when value="off">
419 </when> 571 </when>
443 </when> 595 </when>
444 </conditional> 596 </conditional>
445 597
446 598
447 <conditional name="cTrimLen"> 599 <conditional name="cTrimLen">
448 <param name="select" type="select" label="6) Trimming to length"> 600 <param name="select" type="select" label="7) Trimming to length">
449 <option value="off" selected="true">Off</option> 601 <option value="off" selected="true">Off</option>
450 <option value="on">On</option> 602 <option value="on">On</option>
451 </param> 603 </param>
452 <when value="off"> 604 <when value="off">
453 </when> 605 </when>
454 <when value="on"> 606 <when value="on">
455 <param name="trimLen" size="4" type="integer" value="" label="Length" help="trim reads to certain length from right"/> 607 <param name="trimLen" size="4" type="integer" value="" label="Length" help="trim reads to certain length from right"/>
456 </when> 608 </when>
457 </conditional> 609 </conditional>
458 610
459 <param name="minReadLen" size="4" type="integer" value="20" label="7) Minimum read length"/> 611 <param name="minReadLen" size="4" type="integer" value="20" label="8) Minimum read length"/>
460 612
461 <conditional name="cAddOptions"> 613 <conditional name="cAddOptions">
462 <param name="select" type="select" label="Additional options"> 614 <param name="select" type="select" label="Additional options">
463 <option value="hide" selected="true">Hide</option> 615 <option value="hide" selected="true">Hide</option>
464 <option value="show">Show</option> 616 <option value="show">Show</option>
513 <outputs> 665 <outputs>
514 <data name="outlog" format="txt" label="Flexbar log for ${on_string}"/> 666 <data name="outlog" format="txt" label="Flexbar log for ${on_string}"/>
515 667
516 <data name="rsout" label="Flexbar on ${reads.rs.name}" format_source="rs"> 668 <data name="rsout" label="Flexbar on ${reads.rs.name}" format_source="rs">
517 <filter>reads['mode'] == 'se'</filter> 669 <filter>reads['mode'] == 'se'</filter>
670 <filter>cBarcodes['select'] == "off"</filter>
518 </data> 671 </data>
519 672
520 <data name="r1out" label="Flexbar on ${reads.r1.name}" format_source="r1"> 673 <data name="r1out" label="Flexbar on ${reads.r1.name}" format_source="r1">
521 <filter>reads['mode'] == "pe"</filter> 674 <filter>reads['mode'] == "pe"</filter>
675 <filter>cBarcodes['select'] == "off"</filter>
522 </data> 676 </data>
523 <data name="r2out" label="Flexbar on ${reads.r2.name}" format_source="r2"> 677 <data name="r2out" label="Flexbar on ${reads.r2.name}" format_source="r2">
524 <filter>reads['mode'] == "pe"</filter> 678 <filter>reads['mode'] == "pe"</filter>
679 <filter>cBarcodes['select'] == "off"</filter>
525 </data> 680 </data>
526 681
527 <collection name="rcout" type="paired" label="Flexbar on ${on_string}"> 682 <collection name="rcout" type="paired" label="Flexbar on ${on_string}">
528 <filter>reads['mode'] == "pc"</filter> 683 <filter>reads['mode'] == "pc"</filter>
684 <filter>cBarcodes['select'] == "off"</filter>
529 <data name="forward" label="Flexbar on ${reads.rc.forward.name}" format_source="rc['forward']"/> 685 <data name="forward" label="Flexbar on ${reads.rc.forward.name}" format_source="rc['forward']"/>
530 <data name="reverse" label="Flexbar on ${reads.rc.reverse.name}" format_source="rc['reverse']"/> 686 <data name="reverse" label="Flexbar on ${reads.rc.reverse.name}" format_source="rc['reverse']"/>
531 </collection> 687 </collection>
688
689 <collection type="list" label="Flexbar on ${on_string}" name="barcoded">
690 <filter>cBarcodes['select'] == "on"</filter>
691 <discover_datasets pattern="__designation_and_ext__" directory="flexbar_barcoded" visible="true"/>
692 </collection>
693
532 </outputs> 694 </outputs>
533 695
534 <help> 696 <help>
535 697
536 **Description** 698 **Description**