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comparison trimmomatic.xml @ 16:9a38087e3bfd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
author iuc
date Sun, 14 Jan 2024 11:00:33 +0000
parents 32f1f56bd970
children b9aaed85cbd1
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15:32f1f56bd970 16:9a38087e3bfd
8 <!-- 8 <!--
9 Coreutils required for 'readlink -e' work across platforms 9 Coreutils required for 'readlink -e' work across platforms
10 See similar fix for snpSift 10 See similar fix for snpSift
11 https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9 11 https://github.com/galaxyproject/tools-iuc/commit/b5e2080a7afdea9fa476895693b6115824c6fbb9
12 --> 12 -->
13 <requirement type="package" version="8.25">coreutils</requirement> 13 <requirement type="package" version="9.4">coreutils</requirement>
14 </requirements> 14 </requirements>
15 <command detect_errors="aggressive"><![CDATA[ 15 <command detect_errors="aggressive"><![CDATA[
16 @CONDA_TRIMMOMATIC_JAR_PATH@ && 16 @CONDA_TRIMMOMATIC_JAR_PATH@ &&
17 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ && 17 @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&
18 #if $readtype.single_or_paired == "pair_of_files" 18 #if $readtype.single_or_paired == "pair_of_files"
36 fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext' 36 fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
37 #else 37 #else
38 SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension' 38 SE -threads \${GALAXY_SLOTS:-6} fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
39 #end if 39 #end if
40 ## ILLUMINACLIP option 40 ## ILLUMINACLIP option
41 #if $illuminaclip.do_illuminaclip 41 #if $illuminaclip.do_illuminaclip == "yes"
42 #if $illuminaclip.adapter_type.standard_or_custom == "custom" 42 #if $illuminaclip.adapter_type.standard_or_custom == "custom"
43 #if $readtype.single_or_paired in ["pair_of_files","collection"] 43 #if $readtype.single_or_paired in ["pair_of_files","collection"]
44 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads 44 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads
45 #else 45 #else
46 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold 46 ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
132 <when value="collection"> 132 <when value="collection">
133 <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" /> 133 <param name="fastq_pair" format="fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz" type="data_collection" collection_type="paired" label="Select FASTQ dataset collection with R1/R2 pair" />
134 </when> 134 </when>
135 </conditional> 135 </conditional>
136 <conditional name="illuminaclip"> 136 <conditional name="illuminaclip">
137 <param name="do_illuminaclip" type="boolean" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read" truevalue="yes" falsevalue="no" checked="False" /> 137 <param name="do_illuminaclip" type="select" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read">
138 <option value="no" selected="true">no</option>
139 <option value="yes">yes</option>
140 </param>
138 <when value="yes"> 141 <when value="yes">
139 <conditional name="adapter_type"> 142 <conditional name="adapter_type">
140 <param name="standard_or_custom" type="select" label="Select standard adapter sequences or provide custom?"> 143 <param name="standard_or_custom" type="select" label="Select standard adapter sequences or provide custom?">
141 <option value="standard" selected="true">Standard</option> 144 <option value="standard" selected="true">Standard</option>
142 <option value="custom">Custom</option> 145 <option value="custom">Custom</option>
250 <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log"> 253 <data name="err_file" format="txt" label="${tool.name} on ${on_string} (log file)" from_work_dir="trimmomatic.log">
251 <filter>output_err</filter> 254 <filter>output_err</filter>
252 </data> 255 </data>
253 </outputs> 256 </outputs>
254 <tests> 257 <tests>
255 <test> 258 <test expect_num_outputs="3">
256 <!-- Single-end example --> 259 <!-- Single-end example -->
257 <conditional name="readtype"> 260 <conditional name="readtype">
258 <param name="single_or_paired" value="se" /> 261 <param name="single_or_paired" value="se" />
259 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> 262 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
260 </conditional> 263 </conditional>
261 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> 264 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
262 <param name="output_logs" value="yes" /> 265 <param name="output_logs" value="yes" />
263 <param name="output_err" value="yes" /> 266 <param name="output_err" value="yes" />
264 <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> 267 <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
265 <output name="log_file" file="trimmomatic_se_out1.log" /> 268 <output name="log_file" file="trimmomatic_se_out1.log" />
266 <output name="err_file" file="trimmomatic_se_out1.err" /> 269 <output name="err_file" compare="re_match" file="trimmomatic_se_out1.err.re_match" />
267 </test> 270 </test>
268 <test> 271 <test expect_num_outputs="1">
269 <!-- Single-end example - gzipped --> 272 <!-- Single-end example - gzipped -->
270 <param name="single_or_paired" value="se" /> 273 <param name="single_or_paired" value="se" />
271 <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> 274 <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
272 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> 275 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
273 <output name="fastq_out" file="trimmomatic_se_out1.fastq.gz" /> 276 <output name="fastq_out" file="trimmomatic_se_out1.fastq.gz" />
274 </test> 277 </test>
275 <test> 278 <test expect_num_outputs="4">
276 <!-- Paired-end example - gzipped --> 279 <!-- Paired-end example - gzipped -->
277 <param name="single_or_paired" value="pair_of_files" /> 280 <param name="single_or_paired" value="pair_of_files" />
278 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> 281 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
279 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" /> 282 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" />
280 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> 283 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
281 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq.gz" /> 284 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
282 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" /> 285 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
283 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" /> 286 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
284 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" /> 287 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
285 </test> 288 </test>
286 <test> 289 <test expect_num_outputs="4">
287 <!-- Paired-end example --> 290 <!-- Paired-end example -->
288 <param name="single_or_paired" value="pair_of_files" /> 291 <param name="single_or_paired" value="pair_of_files" />
289 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> 292 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
290 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> 293 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
291 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> 294 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
292 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" /> 295 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />
293 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> 296 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
294 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> 297 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
295 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> 298 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
296 </test> 299 </test>
297 <test> 300 <test expect_num_outputs="4">
298 <!-- Paired-end Illumina 1.3-1.7 quality encoding --> 301 <!-- Paired-end Illumina 1.3-1.7 quality encoding -->
299 <param name="single_or_paired" value="pair_of_files" /> 302 <param name="single_or_paired" value="pair_of_files" />
300 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqillumina" ftype="fastqillumina" /> 303 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqillumina" ftype="fastqillumina" />
301 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqillumina" ftype="fastqillumina" /> 304 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqillumina" ftype="fastqillumina" />
302 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> 305 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
303 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqillumina" /> 306 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqillumina" />
304 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqillumina" /> 307 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqillumina" />
305 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqillumina" /> 308 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqillumina" />
306 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqillumina" /> 309 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqillumina" />
307 </test> 310 </test>
308 <test> 311 <test expect_num_outputs="4">
309 <!-- Paired-end Solexa quality encoding --> 312 <!-- Paired-end Solexa quality encoding -->
310 <param name="single_or_paired" value="pair_of_files" /> 313 <param name="single_or_paired" value="pair_of_files" />
311 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqsolexa" ftype="fastqsolexa" /> 314 <param name="fastq_r1_in" value="Illumina_SG_R1.fastqsolexa" ftype="fastqsolexa" />
312 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqsolexa" ftype="fastqsolexa" /> 315 <param name="fastq_r2_in" value="Illumina_SG_R2.fastqsolexa" ftype="fastqsolexa" />
313 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> 316 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
314 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqsolexa" /> 317 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastqsolexa" />
315 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqsolexa" /> 318 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastqsolexa" />
316 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqsolexa" /> 319 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastqsolexa" />
317 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqsolexa" /> 320 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastqsolexa" />
318 </test> 321 </test>
319 <test> 322 <test expect_num_outputs="1">
320 <!-- Single-end example (cropping) --> 323 <!-- Single-end example (cropping) -->
321 <param name="single_or_paired" value="se" /> 324 <param name="single_or_paired" value="se" />
322 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> 325 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
323 <param name="operations_0|operation|name" value="CROP" /> 326 <param name="operations_0|operation|name" value="CROP" />
324 <param name="operations_0|operation|crop" value="10" /> 327 <param name="operations_0|operation|crop" value="10" />
325 <output name="fastq_out" file="trimmomatic_se_out2.fastq" /> 328 <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
326 </test> 329 </test>
327 <test> 330 <test expect_num_outputs="6">
328 <!-- Paired-end with dataset collection --> 331 <!-- Paired-end with dataset collection -->
329 <param name="single_or_paired" value="collection" /> 332 <param name="single_or_paired" value="collection" />
330 <param name="fastq_pair"> 333 <param name="fastq_pair">
331 <collection type="paired"> 334 <collection type="paired">
332 <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> 335 <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
341 <output_collection name="fastq_out_unpaired" type="paired"> 344 <output_collection name="fastq_out_unpaired" type="paired">
342 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> 345 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
343 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" /> 346 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
344 </output_collection> 347 </output_collection>
345 </test> 348 </test>
346 <test> 349 <test expect_num_outputs="6">
347 <!-- Paired-end with dataset collection - gzipped --> 350 <!-- Paired-end with dataset collection - gzipped -->
348 <param name="single_or_paired" value="collection" /> 351 <param name="single_or_paired" value="collection" />
349 <param name="fastq_pair"> 352 <param name="fastq_pair">
350 <collection type="paired"> 353 <collection type="paired">
351 <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" /> 354 <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
360 <output_collection name="fastq_out_unpaired" type="paired"> 363 <output_collection name="fastq_out_unpaired" type="paired">
361 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" /> 364 <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
362 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" /> 365 <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
363 </output_collection> 366 </output_collection>
364 </test> 367 </test>
365 <test> 368 <test expect_num_outputs="1">
366 <!-- Single-end using AVGQUAL --> 369 <!-- Single-end using AVGQUAL -->
367 <param name="single_or_paired" value="se" /> 370 <param name="single_or_paired" value="se" />
368 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> 371 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
369 <param name="operations_0|operation|name" value="AVGQUAL" /> 372 <param name="operations_0|operation|name" value="AVGQUAL" />
370 <param name="operations_0|operation|avgqual" value="30" /> 373 <param name="operations_0|operation|avgqual" value="30" />
371 <output name="fastq_out" file="trimmomatic_avgqual.fastq" /> 374 <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
372 </test> 375 </test>
373 <test> 376 <test expect_num_outputs="1">
374 <!-- Single-end using MAXINFO --> 377 <!-- Single-end using MAXINFO -->
375 <param name="single_or_paired" value="se" /> 378 <param name="single_or_paired" value="se" />
376 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> 379 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
377 <param name="operations_0|operation|name" value="MAXINFO" /> 380 <param name="operations_0|operation|name" value="MAXINFO" />
378 <param name="operations_0|operation|target_length" value="75" /> 381 <param name="operations_0|operation|target_length" value="75" />
379 <param name="operations_0|operation|strictness" value="0.8" /> 382 <param name="operations_0|operation|strictness" value="0.8" />
380 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" /> 383 <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />
381 </test> 384 </test>
382 <test> 385 <test expect_num_outputs="4">
383 <!-- Paired-end ILLUMINACLIP - this does not check valid clipping --> 386 <!-- Paired-end ILLUMINACLIP - this does not check valid clipping -->
384 <param name="single_or_paired" value="pair_of_files" /> 387 <param name="single_or_paired" value="pair_of_files" />
385 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> 388 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
386 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> 389 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
387 <param name="do_illuminaclip" value="true"/> 390 <param name="do_illuminaclip" value="yes"/>
388 <param name="adapter_fasta" value="TruSeq2-PE.fa"/> 391 <param name="adapter_fasta" value="TruSeq2-PE.fa"/>
389 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> 392 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
390 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" /> 393 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />
391 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> 394 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
392 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> 395 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
393 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" /> 396 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" />
394 </test> 397 </test>
395 <test> 398 <test expect_num_outputs="4">
396 <!-- Paired-end ILLUMINACLIP providing 'custom' adapters - this does not check valid clipping --> 399 <!-- Paired-end ILLUMINACLIP providing 'custom' adapters - this does not check valid clipping -->
397 <param name="single_or_paired" value="pair_of_files" /> 400 <param name="single_or_paired" value="pair_of_files" />
398 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> 401 <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
399 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" /> 402 <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
400 <param name="do_illuminaclip" value="true"/> 403 <param name="do_illuminaclip" value="yes"/>
401 <param name="standard_or_custom" value="custom"/> 404 <param name="standard_or_custom" value="custom"/>
402 <param name="adapter_text" 405 <param name="adapter_text"
403 value=">PrefixPE/1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PrefixPE/2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PCR_Primer1_rc&#10;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT&#10;>PCR_Primer2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer2_rc&#10;AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG&#10;>FlowCell1&#10;TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC&#10;>FlowCell2&#10;TTTTTTTTTTCAAGCAGAAGACGGCATACGA&#10;"/> 406 value=">PrefixPE/1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PrefixPE/2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer1&#10;AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT&#10;>PCR_Primer1_rc&#10;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT&#10;>PCR_Primer2&#10;CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT&#10;>PCR_Primer2_rc&#10;AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG&#10;>FlowCell1&#10;TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC&#10;>FlowCell2&#10;TTTTTTTTTTCAAGCAGAAGACGGCATACGA&#10;"/>
404 <param name="adapter_fasta" value="TruSeq2-PE.fa"/> 407 <param name="adapter_fasta" value="TruSeq2-PE.fa"/>
405 <param name="operations_0|operation|name" value="SLIDINGWINDOW" /> 408 <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
406 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" /> 409 <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />
407 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" /> 410 <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
408 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" /> 411 <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
409 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" /> 412 <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" />
410 </test> 413 </test>
411 <test> 414 <test expect_num_outputs="3">
412 <!-- Quality score test --> 415 <!-- Quality score test -->
413 <conditional name="readtype"> 416 <conditional name="readtype">
414 <param name="single_or_paired" value="se" /> 417 <param name="single_or_paired" value="se" />
415 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" /> 418 <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
416 </conditional> 419 </conditional>
418 <param name="output_logs" value="yes" /> 421 <param name="output_logs" value="yes" />
419 <param name="output_err" value="yes" /> 422 <param name="output_err" value="yes" />
420 <param name="quality_score" value="-phred33"/> 423 <param name="quality_score" value="-phred33"/>
421 <output name="fastq_out" file="trimmomatic_se_out1.fastq" /> 424 <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
422 <output name="log_file" file="trimmomatic_se_out1.log" /> 425 <output name="log_file" file="trimmomatic_se_out1.log" />
423 <output name="err_file" file="trimmomatic_se_out2.err" /> 426 <output name="err_file" compare="re_match" file="trimmomatic_se_out2.err.re_match" />
424 </test> 427 </test>
425 </tests> 428 </tests>
426 <help><![CDATA[ 429 <help><![CDATA[
427 .. class:: infomark 430 .. class:: infomark
428 431
497 500
498 .. class:: infomark 501 .. class:: infomark
499 502
500 **Credits** 503 **Credits**
501 504
502 This Galaxy tool has been developed within the Bioinformatics Core Facility at the 505 This Galaxy tool was originally developed within the Bioinformatics Core
503 University of Manchester, with contributions from Peter van Heusden, Marius 506 Facility at the University of Manchester, with contributions from Peter van
504 van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias Bernt and Cristóbal Gallardo. 507 Heusden, Marius van den Beek, Jelle Scholtalbers, Charles Girardot, Matthias
508 Bernt and Cristóbal Gallardo. It is now maintained as part of the IUC tool
509 collection.
505 510
506 It runs the Trimmomatic program which has been developed 511 It runs the Trimmomatic program which has been developed
507 within Bjorn Usadel's group at RWTH Aachen university. 512 within Bjorn Usadel's group at RWTH Aachen university.
508 513
509 Trimmomatic website (including documentation): 514 Trimmomatic website (including documentation):