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comparison rnaseq/cutadapt/cutadapt.xml @ 11:a712b378e090

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cutadapt added
author jjkoehorst <jasperkoehorst@gmail.com>
date Sat, 21 Feb 2015 16:33:42 +0100
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10:3378d12591ea 11:a712b378e090
1 <tool id="cutadapt" name="Cutadapt" version="1.6">
2 <description>Remove adapter sequences from Fastq/Fasta</description>
3 <requirements>
4 <requirement type="package" version="1.6">cutadapt</requirement>
5 </requirements>
6 <version_command>cutadapt --version</version_command>
7
8 <command>cutadapt
9 #if $input.extension.startswith( "fastq"):
10 --format=fastq
11 #if $input.extension == "fastqillumina":
12 --quality-base=64
13 #end if
14 #if $input.extension == "fastqsolexa":
15 --quality-base=64
16 #end if
17 #else
18 --format=$input.extension
19 #end if
20 #for $a in $adapters
21 #if $a.adapter_source.adapter_source_list == 'prebuilt':
22 --adapter="${a.adapter_source.adapter.fields.name}"='${a.adapter_source.adapter}'
23 #else if str($a.adapter_source.adapter_name) != "":
24 --adapter='${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}'
25 #else
26 --adapter='${a.adapter_source.adapter}'
27 #end if
28 #end for
29
30 $anywhere_adapters_textbox
31
32 #for $aa in $anywhere_adapters
33 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'prebuilt':
34 --anywhere="${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"='${aa.anywhere_adapter_source.anywhere_adapter}'
35 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
36 --anywhere='${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
37 #else
38 --anywhere='${aa.anywhere_adapter_source.anywhere_adapter}'
39 #end if
40 #end for
41 #for $fa in $front_adapters
42 #if $fa.front_adapter_source.front_adapter_source_list == 'prebuilt':
43 --front="${fa.front_adapter_source.front_adapter.fields.name}"='${fa.front_adapter_source.front_adapter}'
44 #else if str($fa.front_adapter_source.front_adapter_name) != "":
45 --front='${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
46 #else
47 --front='${fa.front_adapter_source.front_adapter}'
48 #end if
49 #end for
50 --error-rate=$error_rate
51 --times=$count
52 --overlap=$overlap
53 $no_indels
54 $match_read_wildcards
55
56 #if str( $output_filtering_options.output_filtering) == "filter":
57 $output_filtering_options.discard
58 $output_filtering_options.discard_untrimmed
59 $output_filtering_options.no_trim
60 $output_filtering_options.mask_adapter
61 #if str($output_filtering_options.min) != '0':
62 --minimum-length=$output_filtering_options.min
63 #end if
64 #if str($output_filtering_options.max) != '0':
65 --maximum-length=$output_filtering_options.max
66 #end if
67 #end if
68
69 --output='$output'
70
71 #if $paired_end.paired_end_boolean:
72 --paired-output='$paired_output'
73 #end if
74
75 #if str( $output_params.output_type ) == "additional":
76 #if $output_params.rest_file:
77 --rest-file=$rest_output
78 #end if
79 #if $output_params.wildcard_file:
80 --wildcard-file=$wild_output
81 #end if
82 #if $output_params.too_short_file:
83 --too-short-output=$too_short_output
84 #end if
85 #if $output_params.too_long_file:
86 --too-long-output=$too_long_output
87 #end if
88 #if $output_params.untrimmed_file:
89 --untrimmed-output=$untrimmed_output
90 #if $paired_end.paired_end_boolean:
91 --untrimmed-paired-output=$untrimmed_paired_output
92 #end if
93 #end if
94 #if $output_params.info_file:
95 --info-file=$info_file
96 #end if
97
98 #end if
99
100 #if str( $read_modification_params.read_modification) == "modify":
101 #if str($read_modification_params.quality_cutoff) != '0':
102 --quality-cutoff=$read_modification_params.quality_cutoff
103 #end if
104 #if str($read_modification_params.cut) != '0':
105 --cut=$read_modification_params.cut
106 #end if
107 #if $read_modification_params.prefix != '':
108 --prefix="$read_modification_params.prefix"
109 #end if
110 #if $read_modification_params.suffix != '':
111 --suffix="$read_modification_params.suffix"
112 #end if
113 #if $read_modification_params.length_tag != '':
114 --length-tag="$read_modification_params.length_tag"
115 #end if
116 $read_modification_params.zero_cap
117 #end if
118
119 '$input'
120
121 #if $paired_end.paired_end_boolean:
122 '$input2'
123 #end if
124
125 > $report
126 </command>
127 <inputs>
128 <param format="fastq, fastqsanger, fastqillumina, fastqsolexa, fasta" name="input" type="data" optional="false" label="Fastq file to trim" length="100"/>
129 <conditional name="paired_end">
130 <param name="paired_end_boolean" type="boolean" value="false" label="Track Paired Reads" help="This option will keep a second file synchronized if you use one of the filtering options that discards reads. It will NOT trim adapters off of the second read. You must run Cutadapt a second time on the output of the first run to trim adapters from both reads (see Cutadapt documentation for details)." />
131 <when value="true">
132 <param format="fastq, fastqsanger, fastqillumina, fastqsolexa, fasta" name="input2" type="data" optional="false" label="Paired fastq file (NOT trimmed)" length="100"/>
133 </when>
134 </conditional>
135 <param name="anywhere_adapters_textbox" area="True" size="20x40" type="text" value="-b GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACTAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCGGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGGCGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCATGGCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCATTTTATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCAACAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGAATATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTACGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTAGCTATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTATACATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTCAGAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGACGACATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAATATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTACATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGTAGCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAGAGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGAAAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTTTCGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAATCGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTACAGCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTATAATATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCATTCATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCCGAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGAAGATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCGGCAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCAATCTCGTATGCCGTCTTCTGCTTG -b GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATGCCGTCTTCTGCTTG -b " label="Preset cutadapters, replace by yours if required"/>
136
137 <repeat name="adapters" title="3' Adapters" help="Sequence of an adapter that was ligated to the 3' end. The adapter itself and anything that follows is trimmed.">
138 <conditional name="adapter_source">
139 <param name="adapter_source_list" type="select" label="Source" >
140 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
141 <option value="user">Enter custom sequence</option>
142 </param>
143
144 <when value="user">
145 <param name="adapter_name" size="30" label="Enter custom 3' adapter name (Optional)" type="text" value="" />
146 <param name="adapter" size="30" label="Enter custom 3' adapter sequence" type="text" value="AATTGGCC" />
147 </when>
148
149 <when value="prebuilt">
150 <param name="adapter" type="select" label="Choose 3' adapter">
151 <options from_file="cutadapt_adapters.txt">
152 <column name="name" index="1"/>
153 <column name="value" index="0"/>
154 </options>
155 </param>
156 </when>
157 </conditional>
158 </repeat>
159
160 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that was ligated to the 5' or 3' end. If the adapter is found within the read or overlapping the 3' end of the read, the behavior is the same as for the -a option. If the adapter overlaps the 5' end (beginning of the read), the initial portion of the read matching the adapter is trimmed, but anything that follows is kept. If multiple -a or -b options are given, only the best matching adapter is trimmed.">
161 <conditional name="anywhere_adapter_source">
162 <param name="anywhere_adapter_source_list" type="select" label="Source">
163 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
164 <option value="user">Enter custom sequence</option>
165 </param>
166
167 <when value="user">
168 <param name="anywhere_adapter_name" size="30" label="Enter custom 5' or 3' adapter name (Optional)" type="text" value="" />
169 <param name="anywhere_adapter" size="30" label="Enter custom 5' or 3' adapter sequence" type="text" value="AATTGGCC" />
170 </when>
171 <when value="prebuilt">
172 <param name="anywhere_adapter" type="select" label="Choose 5' or 3' adapter">
173 <options from_file="cutadapt_adapters.txt">
174 <column name="name" index="1"/>
175 <column name="value" index="0"/>
176 </options>
177 </param>
178 </when>
179 </conditional>
180 </repeat>
181
182 <repeat name="front_adapters" title="5' (Front) Adapters" help="Sequence of an adapter that was ligated to the 5' end. If the adapter sequence starts with the character '^', the adapter is 'anchored'. An anchored adapter must appear in its entirety at the 5' end of the read (it is a prefix of the read). A non-anchored adapter may appear partially at the 5' end, or it may occur within the read. If it is found within a read, the sequence preceding the adapter is also trimmed. In all cases the adapter itself is trimmed.">
183 <conditional name="front_adapter_source">
184 <param name="front_adapter_source_list" type="select" label="Source">
185 <option value="prebuilt" selected="true">Standard (select from the list below)</option>
186 <option value="user">Enter custom sequence</option>
187 </param>
188
189 <when value="user">
190 <param name="front_adapter_name" size="30" label="Enter custom 5' adapter name (Optional)" type="text" value="" />
191 <param name="front_adapter" size="30" label="Enter custom 5' adapter sequence" type="text" value="AATTGGCC" />
192 </when>
193 <when value="prebuilt">
194 <param name="front_adapter" type="select" label="Choose 5' adapter">
195 <options from_file="cutadapt_adapters.txt">
196 <column name="name" index="1"/>
197 <column name="value" index="0"/>
198 </options>
199 </param>
200 </when>
201 </conditional>
202 </repeat>
203
204 <param name="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)." />
205 <param name="no_indels" type="boolean" value="false" truevalue="--no-indels" falsevalue="" label="Do not allow indels (Use ONLY with anchored 5' (front) adapters)." help="Do not allow indels in the alignments. That is, allow only mismatches. This option is currently only supported for anchored 5' adapters ('^ADAPTER') (default: both mismatches and indels are allowed)." />
206 <param name="count" type="integer" min="1" value="1" label="Match times" help="Try to remove adapters at most COUNT times. Useful when an adapter gets appended multiple times." />
207 <param name="overlap" type="integer" min="1" value="3" label="Minimum overlap length" help="Minimum overlap length. If the overlap between the adapter and the sequence is shorter than LENGTH, the read is not modified. This reduces the number of bases trimmed purely due to short random adapter matches." />
208 <param name="match_read_wildcards" type="boolean" value="false" truevalue="--match-read-wildcards" falsevalue="" label="Match Read Wildcards" help="Allow 'N's in the read as matches to the adapter." />
209
210 <conditional name="output_filtering_options">
211 <param name="output_filtering" type="select" label="Output filtering options" help="Options for filtering processed reads by those that contain the adapter or by minimum or maximum length">
212 <option value="default">Default (no filtering)</option>
213 <option value="filter">Set Filters</option>
214 </param>
215 <when value="default" />
216 <when value="filter">
217 <param name="discard" type="boolean" value="false" truevalue="--discard" falsevalue="" label="Discard Trimmed Reads" help="Discard reads that contain the adapter instead of trimming them. Use the 'Minimum overlap length' option in order to avoid throwing away too many randomly matching reads!" />
218 <param name="discard_untrimmed" type="boolean" value="false" truevalue="--discard-untrimmed" falsevalue="" label="Discard Untrimmed Reads" help="Discard reads that do not contain the adapter." />
219 <param name="min" type="integer" min="0" optional="true" value="0" label="Minimum length" help="Discard trimmed reads that are shorter than LENGTH. Reads that are too short even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no minimum length." />
220 <param name="max" type="integer" min="0" optional="true" value="0" label="Maximum length" help="Discard trimmed reads that are longer than LENGTH. Reads that are too long even before adapter removal are also discarded. In colorspace, an initial primer is not counted. Value of 0 means no maximum length." />
221 <param name="no_trim" type="boolean" value="false" truevalue="--no-trim" falsevalue="" label="Do not trim adapters" help="Match and redirect reads to output/untrimmed-output as usual, but don't remove the adapters (default: trim the adapters)." />
222 <param name="mask_adapter" type="boolean" value="false" truevalue="--mask-adapter" falsevalue="" label="Mask Adapters" help="Mask adapter bases with 'N' instead of trimming them (default: trim adapters)." />
223 </when>
224 </conditional>
225
226 <conditional name="output_params">
227 <param name="output_type" type="select" label="Additional output options" help="By default all reads will be put in the same file. However, reads with adapters matching in the middle, unmatched reads, and too-short reads can be saved in separate files.">
228 <option value="default">Default</option>
229 <option value="additional">Additional output files</option>
230 </param>
231 <when value="default" />
232 <when value="additional">
233 <param name="info_file" type="boolean" value="false" label="Info File" help="Write information about each read and its adapter matches to a file."/>
234 <param name="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."/>
235 <param name="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."/>
236 <param name="too_short_file" 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)"/>
237 <param name="too_long_file" 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)"/>
238 <param name="untrimmed_file" type="boolean" value="false" label="Untrimmed Reads" help="Write reads that do not contain the adapter to a separate file, instead of writing them to the regular output file. (default: output to same file as trimmed)"/>
239 </when>
240 </conditional>
241
242 <conditional name="read_modification_params">
243 <param name="read_modification" type="select" label="Additional modifications to reads" help="Various options to trim reads based on quality, modify read names and quality scores">
244 <option value="none">No Read Modifications</option>
245 <option value="modify">Set Modification Options</option>
246 </param>
247 <when value="none" />
248 <when value="modify">
249 <param name="cut" type="integer" optional="true" value="0" label="Cut bases from reads before adapter trimming" help="Remove bases from the beginning or end of each read before trimming adapters. If positive, the bases are removed from the beginning of each read. If negative, the bases are removed from the end of each read." />
250 <param name="quality_cutoff" type="integer" min="0" optional="true" value="0" label="Quality cutoff" help="Trim low-quality ends from reads before adapter removal. The algorithm is the same as the one used by BWA (Subtract CUTOFF from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal). Value of 0 means no quality trimming." />
251 <param name="prefix" label="Prefix" type="text" help="Add this prefix to read names" />
252 <param name="suffix" label="Suffix" type="text" help="Add this suffix to read names" />
253 <param name="strip_suffix" label="Strip suffix" type="text" help="Remove this suffix from read names if present." />
254 <param name="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'." />
255 <param name="zero_cap" type="boolean" value="false" label="Change negative quality values to zero (0)" truevalue="--zero-cap" falsevalue="" help="Workaround to avoid segmentation faults in BWA" />
256 </when>
257 </conditional>
258 </inputs>
259
260 <outputs>
261 <data format="txt" name="report" label="${tool.name} on ${on_string} (Report)" />
262 <data format="input" name="output" metadata_source="input" label="${tool.name} on ${on_string} (Reads)"/>
263 <data format="input" name="paired_output" metadata_source="input" label="${tool.name} on ${on_string} (Paired Reads)" >
264 <filter>(paired_end['paired_end_boolean'] is True)</filter>
265 </data>
266 <data format="input" name="rest_output" metadata_source="input" label="${tool.name} on ${on_string} (Rest of Reads)" >
267 <filter>(output_params['output_type'] == "additional")</filter>
268 <filter>(output_params['rest_file'] is True)</filter>
269 </data>
270 <data format="txt" name="wild_output" metadata_source="input" label="${tool.name} on ${on_string} (Wildcard File)" >
271 <filter>(output_params['output_type'] == "additional")</filter>
272 <filter>(output_params['wildcard_file'] is True)</filter>
273 </data>
274 <data format="input" name="too_short_output" metadata_source="input" label="${tool.name} on ${on_string} (Too Short Reads)" >
275 <filter>(output_params['output_type'] == "additional")</filter>
276 <filter>(output_params['too_short_file'] is True)</filter>
277 </data>
278 <data format="input" name="too_long_output" metadata_source="input" label="${tool.name} on ${on_string} (Too Long Reads)" >
279 <filter>(output_params['output_type'] == "additional")</filter>
280 <filter>(output_params['too_long_file'] is True)</filter>
281 </data>
282 <data format="input" name="untrimmed_output" metadata_source="input" label="${tool.name} on ${on_string} (Untrimmed Reads)" >
283 <filter>(output_params['output_type'] == "additional")</filter>
284 <filter>(output_params['untrimmed_file'] is True)</filter>
285 </data>
286 <data format="input" name="untrimmed_paired_output" metadata_source="input" label="${tool.name} on ${on_string} (Untrimmed Paired Reads)" >
287 <filter>(paired_end['paired_end_boolean'] is True)</filter>
288 <filter>(output_params['output_type'] == "additional")</filter>
289 <filter>(output_params['untrimmed_file'] is True)</filter>
290 </data>
291 <data format="txt" name="info_file" metadata_source="input" label="${tool.name} on ${on_string} (Info File)" >
292 <filter>(output_params['output_type'] == "additional")</filter>
293 <filter>(output_params['info_file'] is True)</filter>
294 </data>
295 </outputs>
296
297 <stdio>
298 <exit_code range="1" level="fatal" description="IOError, FormatError, or Interrupt" />
299 <exit_code range="2" level="fatal" description="Invalid options specified" />
300 <exit_code range="3:" level="fatal" description="Unknown error" />
301 </stdio>
302
303 <tests>
304 <test>
305 <param name="input" value="cutadapt_small.fastq" ftype="fastqsanger"/>
306 <param name="adapter_source_list" value="user"/>
307 <param name="adapter" value=""/>
308 <param name="anywhere_adapter_source_list" value="user"/>
309 <param name="anywhere_adapter" value="TTAGACATATCTCCGTCG"/>
310 <param name="front_adapter_source_list" value="user"/>
311 <param name="front_adapter" value=""/>
312 <param name="output_filtering" value="default"/>
313 <param name="read_modification" value="none"/>
314 <param name="output_type" value="default"/>
315 <output name="output" file="cutadapt_small.out"/>
316 </test>
317 <!-- Unable to get tests to function with conditional parameters
318 <test>
319 <param name="input" value="cutadapt_small.fastq" ftype="fastqsanger"/>
320 <param name="adapter_source_list" value="user"/>
321 <param name="adapter" value="TTAGACATATCTCCGTCG"/>
322 <param name="anywhere_adapter_source_list" value="user"/>
323 <param name="anywhere_adapter" value=""/>
324 <param name="front_adapter_source_list" value="user"/>
325 <param name="front_adapter" value=""/>
326 <param name="output_filtering" value="filter"/>
327 <param name="discard" value="true"/>
328 <param name="read_modification" value="none"/>
329 <param name="output_type" value="default"/>
330 <output name="output" file="cutadapt_discard.out"/>
331 </test>
332 <test>
333 <param name="input" value="cutadapt_rest.fa" ftype="fasta"/>
334 <param name="adapter_source_list" value="user"/>
335 <param name="adapter" value="ADAPTER"/>
336 <param name="anywhere_adapter_source_list" value="user"/>
337 <param name="anywhere_adapter" value=""/>
338 <param name="front_adapter_source_list" value="user"/>
339 <param name="front_adapter" value=""/>
340 <param name="output_filtering" value="default"/>
341 <param name="read_modification" value="none"/>
342 <param name="output_type" value="additional"/>
343 <param name="rest_file" value="true"/>
344 <output name="output" file="cutadapt_rest.out"/>
345 <output name="rest_output" file="cutadapt_rest2.out"/>
346 </test>
347 -->
348 </tests>
349
350 <help>
351 Note
352 -------
353 Original code from lparsons, 1% modified to add more reads at once.
354
355 Summary
356 -------
357 This tool removes adapter sequences from DNA high-throughput
358 sequencing data. This is usually necessary when the read length of the
359 machine is longer than the molecule that is sequenced, such as in
360 microRNA data.
361
362 The tool is based on the opensource `cutadapt
363 &lt;http://code.google.com/p/cutadapt/>`_ tool. See the `complete cutadapt
364 documentation &lt;https://cutadapt.readthedocs.org/en/latest/index.html>`_ for additional details.
365
366 -----
367
368 Algorithm
369 ---------
370
371 cutadapt uses a simple semi-global alignment algorithm, without any special optimizations.
372 For speed, the algorithm is implemented as a Python extension module in ``calignmodule.c``.
373
374
375 Partial adapter matches
376 -----------------------
377
378 Cutadapt correctly deals with partial adapter matches. As an example, suppose
379 your adapter sequence is ``ADAPTER`` (specified via 3' Adapters parameter).
380 If you have these input sequences::
381
382 MYSEQUENCEADAPTER
383 MYSEQUENCEADAP
384 MYSEQUENCEADAPTERSOMETHINGELSE
385
386 All of them will be trimmed to ``MYSEQUENCE``. If the sequence starts with an
387 adapter, like this::
388
389 ADAPTERSOMETHING
390
391 It will be empty after trimming.
392
393 When the allowed error rate is sufficiently high, errors in
394 the adapter sequence are allowed. For example, ``ADABTER`` (1 mismatch), ``ADAPTR`` (1 deletion),
395 and ``ADAPPTER`` (1 insertion) will all be recognized if the error rate is set to 0.15.
396
397
398 Anchoring 5' adapters
399 ---------------------
400
401 If you specify a 5' (Front) adapter, the adapter may overlap the beginning of the read or
402 occur anywhere whithin it. If it appears withing the read, the sequence that precedes it
403 will also be trimmed in addition to the adapter. For example when the adapter sequence is
404 ``ADAPTER``::
405
406 HELLOADAPTERTHERE
407 APTERTHERE
408
409 will both be trimmed to ``THERE``. To avoid this, you can prefix the adapter with the character
410 ``^``. This will restrict the search, forcing the adapter to be a prefix of the read. With
411 the adapter sequence set to ``^ADAPTER``, only reads like this will be trimmed::
412
413 ADAPTERHELLO
414
415
416 Allowing adapters anywhere
417 --------------------------
418
419 Cutadapt assumes that any adapter specified via the 3' Adapter parameter
420 was ligated to the 3\' end of the sequence. This is the correct assumption for
421 at least the SOLiD and Illumina small RNA protocols and probably others.
422 The assumption is enforced by the alignment algorithm, which only finds the adapter
423 when its starting position is within the read. In other words, the 5' base of
424 the adapter must appear within the read. The adapter and all bases following
425 it are removed.
426
427 If, on the other hand, your adapter can also be ligated to the 5' end (on
428 purpose or by accident), you should tell cutadapt so by using the Anywhere Adapter
429 parameter. It will then use a slightly different alignment algorithm
430 (so-called semiglobal alignment), which allows any type of overlap between the
431 adapter and the sequence. In particular, the adapter may appear only partially
432 in the beginning of the read, like this::
433
434 PTERMYSEQUENCE
435
436 The decision which part of the read to remove is made as follows: If there is at
437 least one base before the found adapter, then the adapter is considered to be
438 a 3' adapter and the adapter itself and everything following it is removed.
439 Otherwise, the adapter is considered to be a 5' adapter and it is removed from
440 the read.
441
442 Here are some examples, which may make this clearer (left: read, right: trimmed
443 read)::
444
445 MYSEQUENCEADAPTER -> MYSEQUENCE (3' adapter)
446 MADAPTER -> M (3' adapter)
447 ADAPTERMYSEQUENCE -> MYSEQUENCE (5' adapter)
448 PTERMYSEQUENCE -> MYSEQUENCE (5' adapter)
449
450 The regular algorithm (3' Adapter) would trim the first two examples in the same way,
451 but trim the third to an empty sequence and trim the fourth not at all.
452
453
454 Format of the info file
455 -----------------------
456 The info file contains information about the found adapters. The output is a tab-separated text file. Each line corresponds to one read of the input file. The fields are:
457
458 1. Read name
459 2. Number of errors
460 3. 0-based start coordinate of the adapter match
461 4. 0-based end coordinate of the adapter match
462 5. Sequence of the read to the left of the adapter match (can be empty)
463 6. Sequence of the read that was matched to the adapter
464 7. Sequence of the read to the right of the adapter match (can be empty)
465 8. Name of the found adapter.
466
467 The concatenation of the fields 5-7 yields the full read sequence. In column 8, adapters without a name are numbered starting from 1.
468
469 If no adapter was found, the format is as follows:
470
471 1. Read name
472 2. The value -1
473 3. The read sequence
474
475 When parsing that file, be aware that additional columns may be added in the future. Note also that some fields can be empty, resulting in consecutive tabs within a line. Also, in the current version, when the *Match times* option is set to a value other than 1 (the default value), multiple lines are written to the info file for each read.
476
477 .. _cutadapt: http://code.google.com/p/cutadapt/
478 </help>
479
480 </tool>
481