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Adjusted tool definition and wrapper to Flexbar 2.31 release.
author jtilman
date Thu, 17 Jan 2013 18:26:14 +0100
parents 4cbf6c6d2f2b
children 69ddef2ec7d2
comparison
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12:4cbf6c6d2f2b 13:346a2b0979ea
1 1
2 <!-- Author: Johannes T. Roehr --> 2 <!-- Flexbar tool definition for Galaxy, version 2.31 -->
3 3 <!-- Author: Johannes Roehr -->
4 <tool id="flexbar" name="Flexbar" version="2.3" force_history_refresh="True"> 4
5 <tool id="flexbar" name="Flexbar" version="2.31" force_history_refresh="True">
5 6
6 <description>flexible barcode and adapter removal</description> 7 <description>flexible barcode and adapter removal</description>
7 8
8 <requirements> 9 <requirements>
9 <requirement type="binary" version="2.3">flexbar</requirement> 10 <requirement type="binary" version="2.31">flexbar</requirement>
10 </requirements> 11 </requirements>
11 12
12 <version_command>flexbar --version</version_command> 13 <version_command>flexbar --version</version_command>
13 14
14 <command interpreter="perl"> 15 <command interpreter="perl">
124 #end if 125 #end if
125 126
126 127
127 #if $cLogging.select == "show": 128 #if $cLogging.select == "show":
128 $cLogging.logLevel 129 $cLogging.logLevel
129 $cLogging.noLenDist 130 $cLogging.singleReads
130 $cLogging.remTag 131 $cLogging.lenDist
131 #end if 132 $cLogging.fastaOutput
132 133 $cLogging.numTags
133 #if $cLogging.select == "off": 134 $cLogging.remTags
134 --no-length-dist
135 #end if 135 #end if
136 136
137 137
138 $output $output.id $__new_file_path__ $reads.ext 138 $output $output.id $__new_file_path__ $reads.ext
139 139
328 <option value="" selected="true">Off</option> 328 <option value="" selected="true">Off</option>
329 <option value="--log-level ALL">All</option> 329 <option value="--log-level ALL">All</option>
330 <option value="--log-level MOD">Modified</option> 330 <option value="--log-level MOD">Modified</option>
331 <option value="--log-level TAB">Tabular</option> 331 <option value="--log-level TAB">Tabular</option>
332 </param> 332 </param>
333 333
334 <param name="noLenDist" type="select" label="Read length distribution"> 334 <param name="singleReads" type="select" label="Single reads">
335 <option value="--no-length-dist" selected="true">Off</option> 335 <option value="" selected="true">Off</option>
336 <option value="">On</option> 336 <option value="--single-reads">On</option>
337 </param> 337 </param>
338 338
339 <param name="remTag" type="select" label="Read tagging"> 339 <param name="lenDist" type="select" label="Read length distribution">
340 <option value="" selected="true">Off</option> 340 <option value="" selected="true">Off</option>
341 <option value="--removal-tag">Removal tags</option> 341 <option value="--length-dist">On</option>
342 </param> 342 </param>
343 </when> 343
344 </conditional> 344 <param name="fastaOutput" type="select" label="Fasta output">
345 345 <option value="" selected="true">Off</option>
346 <option value="--fasta-output">Always</option>
347 </param>
348
349 <param name="numTags" type="select" label="Number tags">
350 <option value="" selected="true">Off</option>
351 <option value="--number-tags">On</option>
352 </param>
353
354 <param name="remTags" type="select" label="Removal tags">
355 <option value="" selected="true">Off</option>
356 <option value="--removal-tags">On</option>
357 </param>
358 </when>
359 </conditional>
360
346 </inputs> 361 </inputs>
347 362
348 <stdio> 363 <stdio>
349 <exit_code range="1:" level="fatal" description="Error!" /> 364 <exit_code range="1:" level="fatal" description="Error!" />
350 </stdio> 365 </stdio>
351 366
352 <outputs> 367 <outputs>
353 <data format="txt" name="output" metadata_source="reads"/> 368 <data format="txt" name="output" metadata_source="reads"/>
354 </outputs> 369 </outputs>
355 370
356 371
357 <help> 372 <help>
358 **Flexbar help** 373
374 **Flexbar description**
359 375
360 Flexbar_ is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform. 376 Flexbar_ is a program to preprocess sequencing data. It demultiplexes barcoded runs and removes adapter sequences. Further, basic read trimming and filtering options are provided. Flexbar increases mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform.
361 377
362 .. _Flexbar: https://sourceforge.net/projects/flexbar 378 .. _Flexbar: https://sourceforge.net/projects/flexbar
363 379
364 ------ 380 ------
365 381
382 **Trim-end modes**
383
384 **Any:** longer part of read remains
385
386 **Left:** align before or at read end, right part remains
387
388 **Right:** align after or at read start, left part remains
389
390 **Left tail:** consider first n bases, see tail-length options
391
392 **Right tail:** use only last n bases of reads in alignment
393
394 ------
395
366 **Reference** 396 **Reference**
367 397
368 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905. 398 Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich: Flexbar — flexible barcode and adapter processing for next-generation sequencing platforms. Biology 2012, 1(3):895-905.
369
370 ------
371
372 **Trim-end modes**
373
374 **Any:** longer part of read remains
375
376 **Left:** align before or at read end, right part remains
377
378 **Right:** align after or at read start, left part remains
379
380 **Left tail:** consider first n bases, see tail-length options
381
382 **Right tail:** use only last n bases of reads in alignment
383 399
384 ------ 400 ------
385 401
386 **Documentation** 402 **Documentation**
387 403