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comparison cutadapt.xml @ 12:78e1cf88d133 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 195c6112eff237b20a6744e82e2c4e7641f7c488
author iuc
date Thu, 24 May 2018 18:24:08 -0400
parents 8665bcc8b847
children f5fdf41c08b8
comparison
equal deleted inserted replaced
11:8665bcc8b847 12:78e1cf88d133
1 <tool id="cutadapt" name="Cutadapt" version="1.16"> 1 <tool id="cutadapt" name="Cutadapt" version="1.16.1" profile="17.09">
2 <description>Remove adapter sequences from Fastq/Fasta</description> 2 <description>Remove adapter sequences from Fastq/Fasta</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
11 11
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 13
14 ## Link in the input and output files, so Cutadapt can tell their type 14 ## Link in the input and output files, so Cutadapt can tell their type
15 15
16 #set compressed="False" 16 #import re
17 #set format = "fastq" 17 #set format = "fastq"
18 18 #set read1 = "input_f"
19 #if str($library.type) == 'paired': 19 #set read2 = "input_r"
20 20 #set paired = False
21 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): 21 #set library_type = str($library.type)
22 #set read1 = "input_f.fastq.gz" 22 #if $library_type == 'paired':
23 #set compressed = "GZ" 23 #set paired = True
24 #set out1 = "out1.gz" 24 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
25 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): 25 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
26 #set read1 = "input_f.fastq.bz2" 26 #set input_1 = $library.input_1
27 #set compressed = "BZ2" 27 #set input_2 = $library.input_2
28 #set out1 = "out1.bz2" 28 #else if $library_type == 'paired_collection'
29 #else if $library.input_1.is_of_type('fasta'): 29 #set paired = True
30 #set input_1 = $library.input_1.forward
31 #set input_2 = $library.input_1.reverse
32 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name))
33 #else
34 #set input_1 = $library.input_1
35 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
36 #end if
37
38 #if $input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
39 #set read1 = $read1 + ".fq.gz"
40 #set out1 = "out1.gz"
41 #else if $input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
42 #set read1 = $read1 + ".fq.bz2"
43 #set out1 = "out1.bz2"
44 #else if $input_1.is_of_type('fasta'):
45 #set format = "fasta"
46 #set read1 = $read1 + ".fa"
47 #set out1 = "out1.fa"
48 #else:
49 #set read1 = $read1 + ".fq"
50 #set out1 = "out1.fq"
51 #end if
52 ln -f -s '${input_1}' '$read1' &&
53
54 #if $paired:
55 #if $input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
56 #set read2 = $read2 + ".fq.gz"
57 #set out2 = "out2.gz"
58 #else if $input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
59 #set read2 = $read2 + ".fq.bz2"
60 #set out2 = "out2.bz2"
61 #else if $input_2.is_of_type('fasta'):
30 #set format = "fasta" 62 #set format = "fasta"
31 #set read1 = "input_f.fasta" 63 #set read2 = $read2 + ".fa"
32 #set out1 = "out1.fa" 64 #set out2 = "out2.fa"
33 #else: 65 #else:
34 #set read1 = "input_f.fastq" 66 #set read2 = $read2 + ".fq"
35 #set out1 = "out1.fq"
36 #end if
37 ln -f -s '${library.input_1}' ${read1} &&
38
39 #if $library.input_2.is_of_type("fastq.gz", "fastqsanger.gz"):
40 #set read2 = "input_r.fastq.gz"
41 #set compressed = "GZ"
42 #set out2 = "out2.gz"
43 #else if $library.input_2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
44 #set read2 = "input_r.fastq.bz2"
45 #set compressed = "BZ2"
46 #set out2 = "out2.bz2"
47 #else if $library.input_2.is_of_type('fasta'):
48 #set read2 = "input_r.fasta"
49 #set out2 = "out2.fa"
50 #set format = "fasta"
51 #else:
52 #set read2 = "input_r.fastq"
53 #set out2 = "out2.fq" 67 #set out2 = "out2.fq"
54 #end if 68 #end if
55 ln -f -s '${library.input_2}' ${read2} && 69 ln -f -s '${input_2}' '$read2' &&
56 70 #end if
57
58 #else if str($library.type) == 'paired_collection':
59
60 #if $library.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
61 #set read1 = "input_f.fastq.gz"
62 #set compressed = "GZ"
63 #set out1 = "out1.gz"
64 #else if $library.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
65 #set read1 = "input_f.fastq.bz2"
66 #set compressed = "BZ2"
67 #set out1 = "out1.bz2"
68 #else if $library.input_1.forward.is_of_type('fasta'):
69 #set format = "fasta"
70 #set read1 = "input_f.fasta"
71 #set out1 = "out1.fa"
72 #else:
73 #set read1 = "input_f.fastq"
74 #set out1 = "out1.fq"
75 #end if
76 ln -s '${library.input_1.forward}' ${read1} &&
77
78 #if $library.input_1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
79 #set read2 = "input_r.fastq.gz"
80 #set compressed = "GZ"
81 #set out1 = "out2.gz"
82 #else if $library.input_1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
83 #set read2 = "input_r.fastq.bz2"
84 #set compressed = "BZ2"
85 #set out2 = "out2.bz2"
86 #else if $library.input_1.reverse.is_of_type("fasta"):
87 #set format = "fasta"
88 #set read2 = "input_r.fasta"
89 #set out2 = "out2.fa"
90 #else:
91 #set read2 = "input_r.fastq"
92 #set out2 = "out2.fq"
93 #end if
94 ln -s '${library.input_1.reverse}' ${read2} &&
95
96 #else:
97 #if $library.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
98 #set read1 = "input_f.fastq.gz"
99 #set compressed = "GZ"
100 #set out1 = "out1.gz"
101 #else if $library.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
102 #set read1 = "input_f.fastq.bz2"
103 #set compressed = "BZ2"
104 #set out1 = "out1.bz2"
105 #else if $library.input_1.is_of_type('fasta'):
106 #set format = "fasta"
107 #set read1 = "input_f.fasta"
108 #set out1 = "out1.fa"
109 #else:
110 #set read1 = "input_f.fastq"
111 #set out1 = "out1.fq"
112 #end if
113 ln -f -s '${library.input_1}' ${read1} &&
114 #end if
115
116 71
117 ## Run Cutadapt 72 ## Run Cutadapt
118 73
119 cutadapt 74 cutadapt
120 75
177 #end if 132 #end if
178 #if $read_mod_options.length_tag != '': 133 #if $read_mod_options.length_tag != '':
179 --length-tag="$read_mod_options.length_tag" 134 --length-tag="$read_mod_options.length_tag"
180 #end if 135 #end if
181 136
182 #if str( $library.type ) == "single": 137 '${read1}'
183 '${read1}' 138 #if $paired:
184 #else:
185 '${read1}'
186 '${read2}' 139 '${read2}'
187 #end if 140 #end if
188 141
189 #if $output_options.report: 142 #if $output_options.report:
190 > report.txt 143 > report.txt
191 #end if 144 #end if
192
193 ]]></command> 145 ]]></command>
194
195 <inputs> 146 <inputs>
196 147
197 <!-- Reads --> 148 <!-- Reads -->
198 <conditional name="library"> 149 <conditional name="library">
199 <param name="type" type="select" label="Single-end or Paired-end reads?"> 150 <param name="type" type="select" label="Single-end or Paired-end reads?">
215 166
216 <when value="paired_collection"> 167 <when value="paired_collection">
217 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" /> 168 <param name="input_1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2,fasta" type="data_collection" collection_type="paired" label="Paired Collection" help="Should be of datatype &quot;fastq.gz&quot; or &quot;fasta&quot;" />
218 <expand macro="paired_end_options" /> 169 <expand macro="paired_end_options" />
219 </when> 170 </when>
171
220 </conditional> 172 </conditional>
221 173
222 <!-- Adapter Options --> 174 <!-- Adapter Options -->
223 <section name="adapter_options" title="Adapter Options"> 175 <section name="adapter_options" title="Adapter Options">
224 <param name="error_rate" argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." /> 176 <param name="error_rate" argument="--error-rate" type="float" min="0" max="1" value="0.1" label="Maximum error rate" help="Maximum allowed error rate (no. of errors divided by the length of the matching region)." />
259 <param name="length_tag" argument="--length-tag" label="Length Tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." /> 211 <param name="length_tag" argument="--length-tag" label="Length Tag" type="text" help="Search for TAG followed by a decimal number in the name of the read (description/comment field of the FASTA or FASTQ file). Replace the decimal number with the correct length of the trimmed read. For example, use --length-tag 'length=' to search for fields like 'length=123'." />
260 </section> 212 </section>
261 213
262 <!-- Output Options --> 214 <!-- Output Options -->
263 <section name="output_options" title="Output Options"> 215 <section name="output_options" title="Output Options">
264 <param name="report" type="boolean" value="False" label="Report" help="Cutadapt's per-adapter statistics."/> 216 <param name="report" type="boolean" value="False" label="Report" help="Cutadapt's per-adapter statistics. You can use this file with MultiQC."/>
265 <param name="info_file" argument="--info-file" type="boolean" value="False" label="Info File" help="Write information about each read and its adapter matches to a file."/> 217 <param name="info_file" argument="--info-file" type="boolean" value="False" label="Info File" help="Write information about each read and its adapter matches to a file."/>
266 <param name="rest_file" argument="--rest-file" type="boolean" value="False" label="Rest of Read" help="When the adapter matches in the middle of a read, write the rest (after the adapter) into a file."/> 218 <param name="rest_file" argument="--rest-file" type="boolean" value="False" label="Rest of Read" help="When the adapter matches in the middle of a read, write the rest (after the adapter) into a file."/>
267 <param name="wildcard_file" argument="--wildcard-file" type="boolean" value="False" label="Wildcard File" help="When the adapter has wildcard bases ('N's) write adapter bases matching wildcard positions to file."/> 219 <param name="wildcard_file" argument="--wildcard-file" type="boolean" value="False" label="Wildcard File" help="When the adapter has wildcard bases ('N's) write adapter bases matching wildcard positions to file."/>
268 <param name="too_short_file" argument="--too-short-output" type="boolean" value="False" label="Too Short Reads" help="Write reads that are too short (according to minimum length specified) to a file. (default: discard reads)"/> 220 <param name="too_short_file" argument="--too-short-output" type="boolean" value="False" label="Too Short Reads" help="Write reads that are too short (according to minimum length specified) to a file. (default: discard reads)"/>
269 <param name="too_long_file" argument="--too-long-output" type="boolean" value="False" label="Too Long Reads" help="Write reads that are too long (according to maximum length specified) to a file. (default: discard reads)"/> 221 <param name="too_long_file" argument="--too-long-output" type="boolean" value="False" label="Too Long Reads" help="Write reads that are too long (according to maximum length specified) to a file. (default: discard reads)"/>
271 </section> 223 </section>
272 224
273 </inputs> 225 </inputs>
274 226
275 <outputs> 227 <outputs>
276 <data name="out1" format_source="input_1" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output"/> 228 <data name="out1" format="fasta" metadata_source="input_1" from_work_dir="out1*" label="${tool.name} on ${on_string}: Read 1 Output">
277 <data name="out2" format_source="input_2" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" > 229 <expand macro="inherit_format_1" />
230 </data>
231 <data name="out2" format="fastqsanger" metadata_source="input_2" from_work_dir="out2*" label="${tool.name} on ${on_string}: Read 2 Output" >
278 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> 232 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
233 <expand macro="inherit_format_2" />
279 </data> 234 </data>
280 235
281 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report"> 236 <data name="report" format="txt" from_work_dir="report.txt" label="${tool.name} on ${on_string}: Report">
282 <filter>(output_options['report'] is True)</filter> 237 <filter>(output_options['report'] is True)</filter>
283 </data> 238 </data>
284 239
285 <data name="info_file" format_source="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" > 240 <data name="info_file" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Info File" >
286 <filter>(output_options['info_file'] is True)</filter> 241 <filter>(output_options['info_file'] is True)</filter>
287 </data> 242 </data>
288 243
289 <data name="rest_output" format_source="input_1" metadata_source="input_1" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" > 244 <data name="rest_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Rest of Reads (R1 only)" >
290 <filter>(output_options['rest_file'] is True)</filter> 245 <filter>(output_options['rest_file'] is True)</filter>
291 </data> 246 <expand macro="inherit_format_1" />
292 247 </data>
293 <data name="wild_output" format_source="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Wildcard File" > 248
249 <data name="wild_output" format="txt" metadata_source="input_1" label="${tool.name} on ${on_string}: Wildcard File" >
294 <filter>(output_options['wildcard_file'] is True)</filter> 250 <filter>(output_options['wildcard_file'] is True)</filter>
295 </data> 251 </data>
296 252
297 <data name="untrimmed_output" format_source="input_1" metadata_source="input_1" label="${tool.name} on ${on_string}: Untrimmed Read 1" > 253 <data name="untrimmed_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Untrimmed Read 1" >
298 <filter>(output_options['untrimmed_file'] is True)</filter> 254 <filter>(output_options['untrimmed_file'] is True)</filter>
299 </data> 255 <expand macro="inherit_format_1" />
300 <data name="untrimmed_paired_output" format_source="input_2" metadata_source="input_2" label="${tool.name} on ${on_string}: Untrimmed Read 2" > 256 </data>
257 <data name="untrimmed_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Untrimmed Read 2" >
301 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> 258 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
302 <filter>(output_options['untrimmed_file'] is True)</filter> 259 <filter>(output_options['untrimmed_file'] is True)</filter>
303 </data> 260 <expand macro="inherit_format_2" />
304 261 </data>
305 <data name="too_short_output" format_source="input_1" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Short Read 1" > 262
263 <data name="too_short_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Short Read 1" >
306 <filter>(output_options['too_short_file'] is True)</filter> 264 <filter>(output_options['too_short_file'] is True)</filter>
307 </data> 265 <expand macro="inherit_format_1" />
308 <data name="too_short_paired_output" format_source="input_2" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Short Read 2" > 266 </data>
267 <data name="too_short_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Short Read 2" >
309 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> 268 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
310 <filter>(output_options['too_short_file'] is True)</filter> 269 <filter>(output_options['too_short_file'] is True)</filter>
311 </data> 270 <expand macro="inherit_format_2" />
312 271 </data>
313 <data name="too_long_output" format_source="input_1" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Long Read 1" > 272
273 <data name="too_long_output" format="fastqsanger" metadata_source="input_1" label="${tool.name} on ${on_string}: Too Long Read 1" >
314 <filter>(output_options['too_long_file'] is True)</filter> 274 <filter>(output_options['too_long_file'] is True)</filter>
315 </data> 275 <expand macro="inherit_format_1" />
316 <data name="too_long_paired_output" format_source="input_2" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Long Read 2" > 276 </data>
277 <data name="too_long_paired_output" format="fastqsanger" metadata_source="input_2" label="${tool.name} on ${on_string}: Too Long Read 2" >
317 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter> 278 <filter>(library['type'] == 'paired' or library['type'] == 'paired_collection')</filter>
318 <filter>(output_options['too_long_file'] is True)</filter> 279 <filter>(output_options['too_long_file'] is True)</filter>
280 <expand macro="inherit_format_2" />
319 </data> 281 </data>
320 </outputs> 282 </outputs>
321 283
322 <tests> 284 <tests>
323 <!-- Ensure fastq works --> 285 <!-- Ensure fastq works -->
324 <test> 286 <test>
325 <param name="type" value="single" /> 287 <param name="type" value="single" />
326 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 288 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
327 <param name="adapter_source_list" value="user"/> 289 <param name="adapter_source_list" value="user"/>
328 <param name="adapter" value="AGATCGGAAGAGC"/> 290 <param name="adapter" value="AGATCGGAAGAGC"/>
329 <output name="out1" file="cutadapt_small.out"/> 291 <output name="out1" file="cutadapt_small.out" ftype="fastq"/>
330 </test> 292 </test>
331 <!-- Ensure single end fastq.gz works --> 293 <!-- Ensure single end fastq.gz works -->
332 <test> 294 <test>
333 <param name="type" value="single" /> 295 <param name="type" value="single" />
334 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> 296 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
335 <param name="adapter_source_list" value="user"/> 297 <param name="adapter_source_list" value="user"/>
336 <param name="adapter" value="AGATCGGAAGAGC"/> 298 <param name="adapter" value="AGATCGGAAGAGC"/>
337 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz"/> 299 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
338 </test> 300 </test>
339 <!-- Ensure paired end fastq.gz works --> 301 <!-- Ensure paired end fastq.gz works -->
340 <test> 302 <test>
341 <param name="type" value="paired" /> 303 <param name="type" value="paired" />
342 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> 304 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
343 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" /> 305 <param name="input_2" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
344 <param name="adapter_source_list" value="user"/> 306 <param name="adapter_source_list" value="user"/>
345 <param name="adapter" value="AGATCGGAAGAGC"/> 307 <param name="adapter" value="AGATCGGAAGAGC"/>
346 <param name="adapter_source_list2" value="user"/> 308 <param name="adapter_source_list2" value="user"/>
347 <param name="adapter2" value="AGATCGGAAGAGC"/> 309 <param name="adapter2" value="AGATCGGAAGAGC"/>
348 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz"/> 310 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
349 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz"/> 311 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
312 </test>
313 <!-- Ensure paired collection works -->
314 <test>
315 <param name="type" value="paired_collection" />
316 <param name="input_1">
317 <collection type="paired">
318 <element name="forward" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
319 <element name="reverse" ftype="fastq.gz" value="bwa-mem-fastq2.fq.gz" />
320 </collection>
321 </param>
322 <param name="adapter_source_list" value="user"/>
323 <param name="adapter" value="AGATCGGAAGAGC"/>
324 <param name="adapter_source_list2" value="user"/>
325 <param name="adapter2" value="AGATCGGAAGAGC"/>
326 <output name="out1" decompress="True" file="cutadapt_out1.fq.gz" ftype="fastq.gz"/>
327 <output name="out2" decompress="True" file="cutadapt_out2.fq.gz" ftype="fastq.gz"/>
350 </test> 328 </test>
351 <!-- Ensure built-in adapters work --> 329 <!-- Ensure built-in adapters work -->
352 <test> 330 <test>
353 <param name="type" value="single" /> 331 <param name="type" value="single" />
354 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 332 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
355 <param name="adapter_source_list" value="builtin"/> 333 <param name="adapter_source_list" value="builtin"/>
356 <param name="adapter" value="TGTAGGCC"/> 334 <param name="adapter" value="TGTAGGCC"/>
357 <output name="out1" file="cutadapt_builtin.out"/> 335 <output name="out1" file="cutadapt_builtin.out" ftype="fastq"/>
358 </test> 336 </test>
359 <!-- Ensure discard file output works --> 337 <!-- Ensure discard file output works -->
360 <test> 338 <test>
361 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 339 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
362 <param name="adapter_source_list" value="user"/> 340 <param name="adapter_source_list" value="user"/>
363 <param name="adapter" value="TTAGACATATCTCCGTCG"/> 341 <param name="adapter" value="TTAGACATATCTCCGTCG"/>
364 <param name="output_filtering" value="filter"/> 342 <param name="output_filtering" value="filter"/>
365 <param name="discard" value="True"/> 343 <param name="discard" value="True"/>
366 <param name="read_modification" value="none"/> 344 <param name="read_modification" value="none"/>
367 <param name="output_type" value="default"/> 345 <param name="output_type" value="default"/>
368 <output name="out1" file="cutadapt_discard.out"/> 346 <output name="out1" file="cutadapt_discard.out" ftype="fastq"/>
369 </test> 347 </test>
370 <!-- Ensure rest file output works --> 348 <!-- Ensure rest file output works -->
371 <test> 349 <test>
372 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" /> 350 <param name="input_1" ftype="fasta" value="cutadapt_rest.fa" />
373 <param name="adapter_source_list" value="user"/> 351 <param name="adapter_source_list" value="user"/>
374 <param name="adapter" value="AAAGATG"/> 352 <param name="adapter" value="AAAGATG"/>
375 <param name="output_filtering" value="default"/> 353 <param name="output_filtering" value="default"/>
376 <param name="read_modification" value="none"/> 354 <param name="read_modification" value="none"/>
377 <param name="output_type" value="additional"/> 355 <param name="output_type" value="additional"/>
378 <param name="rest_file" value="True"/> 356 <param name="rest_file" value="True"/>
379 <output name="out1" file="cutadapt_rest.out"/> 357 <output name="out1" file="cutadapt_rest.out" ftype="fasta"/>
380 <output name="rest_output" file="cutadapt_rest2.out"/> 358 <output name="rest_output" file="cutadapt_rest2.out" ftype="fasta"/>
381 </test> 359 </test>
382 <!-- Ensure nextseq-trim option works --> 360 <!-- Ensure nextseq-trim option works -->
383 <test> 361 <test>
384 <param name="type" value="single" /> 362 <param name="type" value="single" />
385 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" /> 363 <param name="input_1" ftype="fastq.gz" value="bwa-mem-fastq1.fq.gz" />
386 <param name="adapter_source_list" value="user"/> 364 <param name="adapter_source_list" value="user"/>
387 <param name="adapter" value="AGATCGGAAGAGC"/> 365 <param name="adapter" value="AGATCGGAAGAGC"/>
388 <param name="read_modification" value="modify"/> 366 <param name="read_modification" value="modify"/>
389 <param name="nextseq_trim" value="20" /> 367 <param name="nextseq_trim" value="20" />
390 <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz"/> 368 <output name="out1" decompress="True" file="cutadapt_nextseq_out.fq.gz" ftype="fastq.gz"/>
391 </test> 369 </test>
392 <!-- Ensure Report and Info file output work --> 370 <!-- Ensure Report and Info file output work -->
393 <test> 371 <test>
394 <param name="type" value="single" /> 372 <param name="type" value="single" />
395 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" /> 373 <param name="input_1" ftype="fastq" value="cutadapt_small.fastq" />
396 <param name="adapter_source_list" value="user"/> 374 <param name="adapter_source_list" value="user"/>
397 <param name="adapter" value="AGATCGGAAGAGC"/> 375 <param name="adapter" value="AGATCGGAAGAGC"/>
398 <param name="report" value="True" /> 376 <param name="report" value="True" />
399 <param name="info_file" value="True" /> 377 <param name="info_file" value="True" />
400 <output name="out1" value="cutadapt_small.out"/> 378 <output name="out1" value="cutadapt_small.out" ftype="fastq"/>
401 <output name="report"> 379 <output name="report">
402 <assert_contents> 380 <assert_contents>
403 <has_text text="Summary"/> 381 <has_text text="Summary"/>
404 </assert_contents> 382 </assert_contents>
405 </output> 383 </output>
406 <output name="info_file" value="cutadapt_info_out.txt"/> 384 <output name="info_file" value="cutadapt_info_out.txt" ftype="txt"/>
407 </test> 385 </test>
408 </tests> 386 </tests>
409 387
410 <help><![CDATA[ 388 <help><![CDATA[
411 389