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comparison trim_galore.xml @ 10:b4e39d993fc8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856
author bgruening
date Thu, 20 Apr 2017 09:14:30 -0400
parents 1bfc7254232e
children 80cd83b11214
comparison
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9:1bfc7254232e 10:b4e39d993fc8
1 <tool id="trim_galore" name="Trim Galore!" version="0.4.2"> 1 <tool id="trim_galore" name="Trim Galore!" version="0.4.3" profile="17.01">
2 <!-- Wrapper compatible with Trim Galore! version 0.4 --> 2 <!-- Wrapper compatible with Trim Galore! version 0.4 -->
3 <description>Quality and adapter trimmer of reads</description> 3 <description>Quality and adapter trimmer of reads</description>
4 <macros> 4 <macros>
5 <macro name="adapter_trimming"> 5 <macro name="adapter_trimming">
6 <conditional name="trimming"> 6 <conditional name="trimming">
47 <!-- conda dependency --> 47 <!-- conda dependency -->
48 <requirement type="package" version="1.8.3">cutadapt</requirement> 48 <requirement type="package" version="1.8.3">cutadapt</requirement>
49 <requirement type="package" version="1.8">cutadapt</requirement> 49 <requirement type="package" version="1.8">cutadapt</requirement>
50 </requirements> 50 </requirements>
51 <version_command> 51 <version_command>
52 perl $__tool_directory__/trim_galore --version 52 perl '$__tool_directory__/trim_galore' --version
53 </version_command> 53 </version_command>
54 <command> 54 <command>
55 <![CDATA[ 55 <![CDATA[
56 56
57 ## trim_galore removes .fastq and .fq file extensions of input files. 57 #set compressed = 'no'
58 ## This is essential if Galaxy provides links to files (with real extensions)
59 ## but that behaviour is causing an inconsistency in output filenaming.
60 ## We work around this by linking every file to cwd without file extension
61
62 #if $singlePaired.sPaired == "single": 58 #if $singlePaired.sPaired == "single":
63 #if str($singlePaired.input_singles).endswith(".gz"): 59 #if $singlePaired.input_singles.is_of_type("fastq.gz"):
64 ln -s "${singlePaired.input_singles}" ./input_singles.gz; 60 #set read1 = 'input_1.fastq.gz'
61 #set compressed = 'gz'
65 #else 62 #else
66 ln -s "${singlePaired.input_singles}" ./input_singles; 63 #set read1 = 'input_1.fastq'
67 #end if 64 #end if
65 ln -s '${singlePaired.input_singles}' ${read1} &&
68 #elif $singlePaired.sPaired == "paired": 66 #elif $singlePaired.sPaired == "paired":
69 #if str($singlePaired.input_mate1).endswith(".gz"): 67 #if $singlePaired.input_mate1.is_of_type("fastq.gz"):
70 ln -s "${singlePaired.input_mate1}" ./input_mate1.gz; 68 #set read1 = 'input_1.fastq.gz'
71 ln -s "${singlePaired.input_mate2}" ./input_mate2.gz; 69 #set compressed = 'gz'
72 #else 70 #else
73 ln -s "${singlePaired.input_mate1}" ./input_mate1; 71 #set read1 = 'input_1.fastq'
74 ln -s "${singlePaired.input_mate2}" ./input_mate2; 72 #end if
75 #end if 73 ln -s '${singlePaired.input_mate1}' ${read1} &&
74
75 #if $singlePaired.input_mate2.is_of_type("fastq.gz"):
76 #set read2 = 'input_2.fastq.gz'
77 #else
78 #set read2 = 'input_2.fastq'
79 #end if
80 ln -s '${singlePaired.input_mate2}' ${read2} &&
76 #else: 81 #else:
77 #if str($singlePaired.input_mate_pairs.forward).endswith(".gz"): 82 #if $singlePaired.input_mate_pairs.forward.is_of_type("fastq.gz"):
78 ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1.gz; 83 #set read1 = 'input_1.fastq.gz'
79 ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2.gz; 84 #set compressed = 'gz'
80 #else 85 #else
81 ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1; 86 #set read1 = 'input_1.fastq'
82 ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2; 87 #end if
83 #end if 88 ln -s '${singlePaired.input_mate_pairs.forward}' ${read1} &&
84 #end if 89
85 90 #if $singlePaired.input_mate_pairs.reverse.is_of_type("fastq.gz"):
86 perl $__tool_directory__/trim_galore 91 #set read2 = 'input_2.fastq.gz'
92 #else
93 #set read2 = 'input_2.fastq'
94 #end if
95 ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} &&
96 #end if
97
98 perl '$__tool_directory__/trim_galore'
87 99
88 ## we only support fastqsanger 100 ## we only support fastqsanger
89 --phred33 101 --phred33
90 102
91 #if $params.settingsType == "custom": 103 #if $params.settingsType == "custom":
145 --three_prime_clip_R1 $singlePaired.three_prime_clip_R1 157 --three_prime_clip_R1 $singlePaired.three_prime_clip_R1
146 #end if 158 #end if
147 159
148 #if $singlePaired.sPaired == "single": 160 #if $singlePaired.sPaired == "single":
149 ## input sequence 161 ## input sequence
150 #if str($singlePaired.input_singles).endswith(".gz"): 162 ${read1}
151 ./input_singles.gz
152 --dont_gzip
153 #else
154 ./input_singles
155 #end if
156 #else: 163 #else:
157 --paired 164 --paired
158 165
159 $singlePaired.trim1 166 $singlePaired.trim1
160 167
167 #if $singlePaired.three_prime_clip_R2: 174 #if $singlePaired.three_prime_clip_R2:
168 --three_prime_clip_R2 $singlePaired.three_prime_clip_R2 175 --three_prime_clip_R2 $singlePaired.three_prime_clip_R2
169 #end if 176 #end if
170 177
171 ## input sequences 178 ## input sequences
172 #if $singlePaired.sPaired == "paired": 179 ${read1}
173 #if str($singlePaired.input_mate1).endswith(".gz"): 180 ${read2}
174 ./input_mate1.gz 181 #end if
175 ./input_mate2.gz 182
176 --dont_gzip 183 #if $compressed == 'no':
177 #else 184 --dont_gzip
178 ./input_mate1
179 ./input_mate2
180 #end if
181 #else:
182 #if str($singlePaired.input_mate_pairs.forward).endswith(".gz"):
183 ./input_mate1.gz
184 ./input_mate2.gz
185 --dont_gzip
186 #else
187 ./input_mate1
188 ./input_mate2
189 #end if
190 #end if
191
192 #end if 185 #end if
193 186
194 ## Trim Galore is finished, rename the output if compressed 187 ## Trim Galore is finished, rename the output if compressed
195 && 188 &&
196 if [ -f input_singles.gz_trimmed.fq ] ; then mv input_singles.gz_trimmed.fq input_singles_trimmed.fq ; fi 189 if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi
197 && 190 &&
198 if [ -f input_mate1.gz_val_1.fq ] ; then mv input_mate1.gz_val_1.fq input_mate1_val_1.fq ; fi 191 if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi
199 && 192 &&
200 if [ -f input_mate2.gz_val_2.fq ] ; then mv input_mate2.gz_val_2.fq input_mate2_val_2.fq ; fi 193 if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi
201 && 194 &&
202 if [ -f input_mate1.gz_unpaired_1.fq ] ; then mv input_mate1.gz_unpaired_1.fq input_mate1_unpaired_1.fq ; fi 195 if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi
203 && 196 &&
204 if [ -f input_mate2.gz_unpaired_2.fq ] ; then mv input_mate2.gz_unpaired_2.fq input_mate2_unpaired_2.fq ; fi 197 if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
205 198
206 ## Trim Galore! run is finished. Move the report files to the proper place 199 ## Trim Galore! run is finished. Move the report files to the proper place
207 #if $params.settingsType == "custom" and $params.report: 200 #if $params.settingsType == "custom" and $params.report:
208 && 201 &&
209 cat ./*_trimming_report.txt > $report_file; 202 cat ./*_trimming_report.txt > $report_file;
218 <option value="single">Single-end</option> 211 <option value="single">Single-end</option>
219 <option value="paired">Paired-end</option> 212 <option value="paired">Paired-end</option>
220 <option value="paired_collection">Paired Collection</option> 213 <option value="paired_collection">Paired Collection</option>
221 </param> 214 </param>
222 <when value="single"> 215 <when value="single">
223 <param name="input_singles" type="data" format="fastqsanger" label="Reads in FASTQ format" /> 216 <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
224 <expand macro="adapter_trimming"/> 217 <expand macro="adapter_trimming"/>
225 218
226 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end"> 219 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end">
227 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed. 220 <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed.
228 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. 221 This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality.
229 (--three_prime_clip_R1)</help> 222 (--three_prime_clip_R1)</help>
230 </param> 223 </param>
231 </when> 224 </when>
232 <when value="paired"> 225 <when value="paired">
233 <param name="input_mate1" type="data" format="fastqsanger" label="Reads in FASTQ format" /> 226 <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
234 <param name="input_mate2" type="data" format="fastqsanger" label="Reads in FASTQ format" /> 227 <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
235 <expand macro="paired_adapter_trimming" /> 228 <expand macro="paired_adapter_trimming" />
236 </when> 229 </when>
237 <when value="paired_collection"> 230 <when value="paired_collection">
238 <param name="input_mate_pairs" format="fastqsanger" type="data_collection" collection_type="paired" 231 <param name="input_mate_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired"
239 label="Select a paired collection" help="See help section for an explanation of dataset collections"/> 232 label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
240 <expand macro="paired_adapter_trimming" /> 233 <expand macro="paired_adapter_trimming" />
241 </when> 234 </when>
242 </conditional> 235 </conditional>
243 236
291 </when> <!-- full --> 284 </when> <!-- full -->
292 </conditional> <!-- params --> 285 </conditional> <!-- params -->
293 286
294 </inputs> 287 </inputs>
295 <outputs> 288 <outputs>
296 <data format="fastqsanger" name="trimmed_reads_single" from_work_dir="input_singles_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads"> 289 <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
297 <filter>singlePaired['sPaired'] == "single"</filter> 290 <filter>singlePaired['sPaired'] == "single"</filter>
298 </data> 291 </data>
299 292
300 <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads"> 293 <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads">
301 <data name="forward" format="fastqsanger" from_work_dir="input_mate1_val_1.fq" /> 294 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_val_1.fq" />
302 <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_val_2.fq" /> 295 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_val_2.fq" />
303 <filter>singlePaired['sPaired'] == "paired_collection"</filter> 296 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
304 </collection> 297 </collection>
305 298
306 <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads"> 299 <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads">
307 <data name="forward" format="fastqsanger" from_work_dir="input_mate1_unpaired_1.fq" /> 300 <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_unpaired_1.fq" />
308 <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_unpaired_2.fq" /> 301 <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_unpaired_2.fq" />
309 <filter>params['settingsType'] == "custom"</filter> 302 <filter>params['settingsType'] == "custom"</filter>
310 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> 303 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
311 <filter>singlePaired['sPaired'] == "paired_collection"</filter> 304 <filter>singlePaired['sPaired'] == "paired_collection"</filter>
312 </collection> 305 </collection>
313 306
314 <data format="fastqsanger" name="trimmed_reads_pair1" from_work_dir="input_mate1_val_1.fq" 307 <data format_source="input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"
315 label="${tool.name} on ${on_string}: trimmed reads pair 1"> 308 label="${tool.name} on ${on_string}: trimmed reads pair 1">
316 <filter>singlePaired['sPaired'] == "paired"</filter> 309 <filter>singlePaired['sPaired'] == "paired"</filter>
317 </data> 310 </data>
318 311
319 <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq" 312 <data format_source="input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"
320 label="${tool.name} on ${on_string}: trimmed reads pair 2"> 313 label="${tool.name} on ${on_string}: trimmed reads pair 2">
321 <filter>singlePaired['sPaired'] == "paired"</filter> 314 <filter>singlePaired['sPaired'] == "paired"</filter>
322 </data> 315 </data>
323 316
324 <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_unpaired_1.fq" 317 <data format_source="input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"
325 label="${tool.name} on ${on_string}: unpaired reads (1)"> 318 label="${tool.name} on ${on_string}: unpaired reads (1)">
326 <filter>params['settingsType'] == "custom"</filter> 319 <filter>params['settingsType'] == "custom"</filter>
327 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> 320 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
328 <filter>singlePaired['sPaired'] == "paired"</filter> 321 <filter>singlePaired['sPaired'] == "paired"</filter>
329 </data> 322 </data>
330 323
331 <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_unpaired_2.fq" 324 <data format_source="input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"
332 label="${tool.name} on ${on_string}: unpaired reads (2)"> 325 label="${tool.name} on ${on_string}: unpaired reads (2)">
333 <filter>params['settingsType'] == "custom"</filter> 326 <filter>params['settingsType'] == "custom"</filter>
334 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> 327 <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
335 <filter>singlePaired['sPaired'] == "paired"</filter> 328 <filter>singlePaired['sPaired'] == "paired"</filter>
336 </data> 329 </data>
347 <param name="settingsType" value="custom" /> 340 <param name="settingsType" value="custom" />
348 <param name="report" value="true" /> 341 <param name="report" value="true" />
349 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/> 342 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/>
350 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="8" /> 343 <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="8" />
351 </test> 344 </test>
345 <test>
346 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
347 <param name="sPaired" value="single" />
348 <param name="settingsType" value="custom" />
349 <param name="report" value="true" />
350 <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
351 <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="9" />
352 </test>
352 353
353 <test> 354 <test>
354 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 355 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
355 <param name="sPaired" value="single" /> 356 <param name="sPaired" value="single" />
356 <param name="trimming_select" value="--illumina" /> 357 <param name="trimming_select" value="--illumina" />
357 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/> 358 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
358 </test> 359 </test>
360 <test>
361 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
362 <param name="sPaired" value="single" />
363 <param name="trimming_select" value="--illumina" />
364 <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
365 </test>
359 366
360 <test> 367 <test>
361 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 368 <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
362 <param name="sPaired" value="single" /> 369 <param name="sPaired" value="single" />
363 <param name="adapter" value="AAAGAGC" /> 370 <param name="adapter" value="AAAGAGC" />
364 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/> 371 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
372 </test>
373 <test>
374 <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
375 <param name="sPaired" value="single" />
376 <param name="adapter" value="AAAGAGC" />
377 <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
365 </test> 378 </test>
366 379
367 <test> 380 <test>
368 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 381 <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
369 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> 382 <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" />
372 <param name="report" value="true" /> 385 <param name="report" value="true" />
373 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/> 386 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/>
374 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/> 387 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>
375 <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" /> 388 <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" />
376 </test> 389 </test>
390 <test>
391 <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
392 <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
393 <param name="sPaired" value="paired" />
394 <param name="settingsType" value="custom" />
395 <param name="report" value="true" />
396 <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
397 <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
398 <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
399 </test>
377 400
378 <test> 401 <test>
379 <param name="input_mate_pairs"> 402 <param name="input_mate_pairs">
380 <collection type="paired"> 403 <collection type="paired">
381 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> 404 <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
397 420
398 <output_collection name="trimmed_reads_unpaired_collection" type="paired"> 421 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
399 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/> 422 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>
400 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/> 423 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>
401 </output_collection> 424 </output_collection>
402 425 </test>
426 <test>
427 <param name="input_mate_pairs">
428 <collection type="paired">
429 <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
430 <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
431 </collection>
432 </param>
433
434 <param name="sPaired" value="paired_collection" />
435 <param name="settingsType" value="custom" />
436 <param name="report" value="true" />
437 <param name="retain_unpaired_select" value="retain_unpaired_output" />
438
439 <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
440
441 <output_collection name="trimmed_reads_paired_collection" type="paired">
442 <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
443 <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
444 </output_collection>
445
446 <output_collection name="trimmed_reads_unpaired_collection" type="paired">
447 <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
448 <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
449 </output_collection>
403 </test> 450 </test>
404 </tests> 451 </tests>
405 <help> 452 <help>
406 <![CDATA[ 453 <![CDATA[
407 **What it does** 454 **What it does**
441 | 488 |
442 | *option --nextera* 489 | *option --nextera*
443 490
444 * **Illumina small RNA adapters** 491 * **Illumina small RNA adapters**
445 492
446 | Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3' Adapter 'TGGAATTCTCGG' instead of the default auto-detection of adapter sequence. Selecting to trim smallRNA adapters will also lower the --length value to 18bp. If the smallRNA libraries are paired-end then -a2 will be set to the Illumina small RNA 5' adapter automatically (‘GATCGTCGGACT’) unless -a 2 had been defined explicitly. 493 | Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3' Adapter 'TGGAATTCTCGG' instead of the default auto-detection of adapter sequence. Selecting to trim smallRNA adapters will also lower the --length value to 18bp. If the smallRNA libraries are paired-end then -a2 will be set to the Illumina small RNA 5' adapter automatically ('GATCGTCGGACT') unless -a 2 had been defined explicitly.
447 | 494 |
448 | *option --small_rna* 495 | *option --small_rna*
449 496
450 * **User defined adapter trimming** 497 * **User defined adapter trimming**
451 498