Mercurial > repos > jtilman > flexbar
comparison flexbar.xml @ 36:4e47e1caf21a draft
Uploaded
author | jtilman |
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date | Thu, 28 Jun 2018 09:11:58 -0400 |
parents | 4a095317caca |
children | 497da23fee84 |
comparison
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35:cb6423bc1097 | 36:4e47e1caf21a |
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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> |