comparison flexbar.xml @ 36:4e47e1caf21a draft

Uploaded
author jtilman
date Thu, 28 Jun 2018 09:11:58 -0400
parents 4a095317caca
children 497da23fee84
comparison
equal deleted inserted replaced
35:cb6423bc1097 36:4e47e1caf21a
90 --qtrim-threshold $cTrimQual.trimQualBWA 90 --qtrim-threshold $cTrimQual.trimQualBWA
91 $cTrimQual.trimQualPostBWA 91 $cTrimQual.trimQualPostBWA
92 #end if 92 #end if
93 93
94 94
95 #if $cTrimLen.select == "on":
96 --post-trim-length $cTrimLen.trimLen
97 #end if
98
99
100 #if $cAdapters.select == "on": 95 #if $cAdapters.select == "on":
101 96
102 #if $cAdapters.ccAdapters.select == "file": 97 #if $cAdapters.ccAdapters.select == "file":
103 --adapters '$cAdapters.ccAdapters.adapterFile' 98 --adapters '$cAdapters.ccAdapters.adapterFile'
104 #end if 99 #end if
145 --adapter-mismatch $cAdapters.aAdvanced.caAlignScores.aMismatch 140 --adapter-mismatch $cAdapters.aAdvanced.caAlignScores.aMismatch
146 --adapter-gap $cAdapters.aAdvanced.caAlignScores.aGap 141 --adapter-gap $cAdapters.aAdvanced.caAlignScores.aGap
147 #end if 142 #end if
148 #end if 143 #end if
149 144
145
146 #if $hTrim.select == "on":
147 #if $hTrim.hTrimLeft != "":
148 --htrim-left $hTrim.hTrimLeft
149 #end if
150 #if $hTrim.hTrimRight != "":
151 --htrim-right $hTrim.hTrimRight
152 #end if
153
154 --htrim-min-length $hTrim.hMinLength
155 --htrim-error-rate $hTrim.hErrorRate
156
157 #if $hTrim.hAdvanced.hMinLength2 != "":
158 --htrim-min-length2 $hTrim.hAdvanced.hMinLength2
159 #end if
160 #if $hTrim.hAdvanced.hMaxLength != "":
161 --htrim-max-length $hTrim.hAdvanced.hMaxLength
162 #end if
163
164 $hTrim.hAdvanced.hMaxFirst
165 $hTrim.hAdvanced.hTrimAdapter
166 #end if
167
168
169 #if $cTrimLen.select == "on":
170 --post-trim-length $cTrimLen.trimLen
171 #end if
150 172
151 #if $cAddOptions.select == "show": 173 #if $cAddOptions.select == "show":
152 $cAddOptions.logLevel 174 $cAddOptions.logLevel
153 $cAddOptions.numTags 175 $cAddOptions.numTags
154 $cAddOptions.remTags 176 $cAddOptions.remTags
351 </when> 373 </when>
352 </conditional> 374 </conditional>
353 375
354 376
355 <param name="aReadSet" type="select" label="Removal for single read set"> 377 <param name="aReadSet" type="select" label="Removal for single read set">
356 <option value="" selected="true">No</option> 378 <option value="" selected="true">Off</option>
357 <option value="--adapter-read-set 1">1st</option> 379 <option value="--adapter-read-set 1">1st</option>
358 <option value="--adapter-read-set 2">2nd</option> 380 <option value="--adapter-read-set 2">2nd</option>
359 </param> 381 </param>
360 382
361 <param name="aCycles" size="4" type="integer" value="1" label="Number of removal cycles"/> 383 <param name="aCycles" size="4" type="integer" value="1" label="Number of removal cycles"/>
376 </section> 398 </section>
377 </when> 399 </when>
378 </conditional> 400 </conditional>
379 401
380 402
381 <conditional name="cTrimLen"> 403 <conditional name="hTrim">
382 <param name="select" type="select" label="5) Trimming to length"> 404 <param name="select" type="select" label="5) Trimming of homopolymers">
383 <option value="off" selected="true">Off</option> 405 <option value="off" selected="true">Off</option>
384 <option value="on">On</option> 406 <option value="on">On</option>
385 </param> 407 </param>
386 <when value="off"> 408 <when value="off">
387 </when> 409 </when>
388 <when value="on"> 410 <when value="on">
411 <param name="hTrimLeft" size="4" label="Trim homopolymers on left end" type="text" value="" optional="true"/>
412 <param name="hTrimRight" size="4" label="Trim homopolymers on right end" type="text" value="" optional="true" help="for example AT"/>
413
414 <param name="hMinLength" size="4" type="integer" value="3" label="Minimum length"/>
415 <param name="hErrorRate" size="4" type="float" value="0.1" label="Error rate"/>
416
417 <section name="hAdvanced" title="Advanced options" expanded="false">
418
419 <param name="hMaxLength" size="4" type="integer" value="" label="Maximum length" optional="true"/>
420
421 <param name="hMaxFirst" type="select" label="Maximum length only for first one">
422 <option value="" selected="true">Off</option>
423 <option value="--htrim-max-first">On</option>
424 </param>
425
426 <param name="hMinLength2" size="4" type="integer" value="" label="Minimum length after first one" optional="true"/>
427
428 <param name="hTrimAdapter" type="select" label="Only in case of adapter on same side">
429 <option value="" selected="true">Off</option>
430 <option value="--htrim-adapter">On</option>
431 </param>
432 </section>
433 </when>
434 </conditional>
435
436
437 <conditional name="cTrimLen">
438 <param name="select" type="select" label="6) Trimming to length">
439 <option value="off" selected="true">Off</option>
440 <option value="on">On</option>
441 </param>
442 <when value="off">
443 </when>
444 <when value="on">
389 <param name="trimLen" size="4" type="integer" value="" label="Length" help="trim reads to certain length from right"/> 445 <param name="trimLen" size="4" type="integer" value="" label="Length" help="trim reads to certain length from right"/>
390 </when> 446 </when>
391 </conditional> 447 </conditional>
392 448
393 <param name="minReadLen" size="4" type="integer" value="20" label="6) Minimum read length"/> 449 <param name="minReadLen" size="4" type="integer" value="20" label="7) Minimum read length"/>
394 450
395 <conditional name="cAddOptions"> 451 <conditional name="cAddOptions">
396 <param name="select" type="select" label="Additional options"> 452 <param name="select" type="select" label="Additional options">
397 <option value="hide" selected="true">Hide</option> 453 <option value="hide" selected="true">Hide</option>
398 <option value="show">Show</option> 454 <option value="show">Show</option>