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comparison qiime2/qiime_cutadapt_trim-paired.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired"
3 version="2020.8">
4 <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime cutadapt trim-paired
10
11 --i-demultiplexed-sequences=$idemultiplexedsequences
12
13 --p-cores=$pcores
14
15 #if str($padapterf):
16 --p-adapter-f=$padapterf
17 #end if
18 #if str($pfrontf):
19 --p-front-f=$pfrontf
20 #end if
21 #if '__ob__' in str($panywheref):
22 #set $panywheref_temp = $panywheref.replace('__ob__', '[')
23 #set $panywheref = $panywheref_temp
24 #end if
25 #if '__cb__' in str($panywheref):
26 #set $panywheref_temp = $panywheref.replace('__cb__', ']')
27 #set $panywheref = $panywheref_temp
28 #end if
29 #if 'X' in str($panywheref):
30 #set $panywheref_temp = $panywheref.replace('X', '\\')
31 #set $panywheref = $panywheref_temp
32 #end if
33 #if '__sq__' in str($panywheref):
34 #set $panywheref_temp = $panywheref.replace('__sq__', "'")
35 #set $panywheref = $panywheref_temp
36 #end if
37 #if '__db__' in str($panywheref):
38 #set $panywheref_temp = $panywheref.replace('__db__', '"')
39 #set $panywheref = $panywheref_temp
40 #end if
41
42 #if str($panywheref):
43 --p-anywhere-f=$panywheref
44 #end if
45
46 #if str($padapterr):
47 --p-adapter-r=$padapterr
48 #end if
49 #if str($pfrontr):
50 --p-front-r=$pfrontr
51 #end if
52 #if '__ob__' in str($panywherer):
53 #set $panywherer_temp = $panywherer.replace('__ob__', '[')
54 #set $panywherer = $panywherer_temp
55 #end if
56 #if '__cb__' in str($panywherer):
57 #set $panywherer_temp = $panywherer.replace('__cb__', ']')
58 #set $panywherer = $panywherer_temp
59 #end if
60 #if 'X' in str($panywherer):
61 #set $panywherer_temp = $panywherer.replace('X', '\\')
62 #set $panywherer = $panywherer_temp
63 #end if
64 #if '__sq__' in str($panywherer):
65 #set $panywherer_temp = $panywherer.replace('__sq__', "'")
66 #set $panywherer = $panywherer_temp
67 #end if
68 #if '__db__' in str($panywherer):
69 #set $panywherer_temp = $panywherer.replace('__db__', '"')
70 #set $panywherer = $panywherer_temp
71 #end if
72
73 #if str($panywherer):
74 --p-anywhere-r=$panywherer
75 #end if
76
77 --p-error-rate=$perrorrate
78
79 #if $pnoindels:
80 --p-no-indels
81 #end if
82
83 --p-times=$ptimes
84
85 --p-overlap=$poverlap
86
87 #if $pmatchreadwildcards:
88 --p-match-read-wildcards
89 #end if
90
91 #if $pnomatchadapterwildcards:
92 --p-no-match-adapter-wildcards
93 #end if
94
95 --p-minimum-length=$pminimumlength
96
97 #if $pdiscarduntrimmed:
98 --p-discard-untrimmed
99 #end if
100
101 --o-trimmed-sequences=otrimmedsequences
102
103 #if str($examples) != 'None':
104 --examples=$examples
105 #end if
106
107 ;
108 cp otrimmedsequences.qza $otrimmedsequences
109
110 ]]></command>
111 <inputs>
112 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data" />
113 <param label="--p-adapter-f: TEXT... Sequence of an adapter ligated to the 3\' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in forward read. If your sequence of interest is \'framed\' by a 5\' and a 3\' adapter, use this parameter to define a \'linked\' primer - see https://cutadapt.readthedocs.io for complete details. [optional]" name="padapterf" optional="False" type="text" value="False" />
114 <param label="--p-front-f: TEXT... Sequence of an adapter ligated to the 5\' end. The List[Str] adapter and any preceding bases are trimmed. Partial matches at the 5\' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in forward read. [optional]" name="pfrontf" optional="False" type="text" />
115 <param label="--p-anywhere-f: TEXT... Sequence of an adapter that may be ligated to the List[Str] 5\' or 3\' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in forward read. [optional]" name="panywheref" optional="False" type="text" />
116 <param label="--p-adapter-r: TEXT... Sequence of an adapter ligated to the 3\' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in reverse read. If your sequence of interest is \'framed\' by a 5\' and a 3\' adapter, use this parameter to define a \'linked\' primer - see https://cutadapt.readthedocs.io for complete details. [optional]" name="padapterr" optional="False" type="text" value="False" />
117 <param label="--p-front-r: TEXT... Sequence of an adapter ligated to the 5\' end. The List[Str] adapter and any preceding bases are trimmed. Partial matches at the 5\' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in reverse read. [optional]" name="pfrontr" optional="False" type="text" />
118 <param label="--p-anywhere-r: TEXT... Sequence of an adapter that may be ligated to the List[Str] 5\' or 3\' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in reverse read. [optional]" name="panywherer" optional="False" type="text" />
119 <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate. [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
120 <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: True]" name="pnoindels" selected="False" type="boolean" />
121 <param label="--p-times: INTEGER Remove multiple occurrences of an adapter if it is Range(1, None) repeated, up to `times` times. [default: 1]" min="1" name="ptimes" optional="True" type="integer" value="1" />
122 <param label="--p-overlap: INTEGER Require at least `overlap` bases of overlap between Range(1, None) read and adapter for an adapter to be found. [default: 3]" min="1" name="poverlap" optional="True" type="integer" value="3" />
123 <param label="--p-match-read-wildcards: --p-match-read-wildcards: / --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" selected="False" type="boolean" />
124 <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pnomatchadapterwildcards" selected="False" type="boolean" />
125 <param label="--p-minimum-length: INTEGER Range(1, None) Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
126 <param label="--p-discard-untrimmed: --p-discard-untrimmed: / --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean" />
127 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
128
129 </inputs>
130
131 <outputs>
132 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences" />
133
134 </outputs>
135
136 <help><![CDATA[
137 Find and remove adapters in demultiplexed paired-end sequences.
138 ###############################################################
139
140 Search demultiplexed paired-end sequences for adapters and remove them. The
141 parameter descriptions in this method are adapted from the official
142 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
143 for complete details.
144
145 Parameters
146 ----------
147 demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
148 The paired-end sequences to be trimmed.
149 cores : Int % Range(1, None), optional
150 Number of CPU cores to use.
151 adapter_f : List[Str], optional
152 Sequence of an adapter ligated to the 3' end. The adapter and any
153 subsequent bases are trimmed. If a `$` is appended, the adapter is only
154 found if it is at the end of the read. Search in forward read. If your
155 sequence of interest is "framed" by a 5' and a 3' adapter, use this
156 parameter to define a "linked" primer - see
157 https://cutadapt.readthedocs.io for complete details.
158 front_f : List[Str], optional
159 Sequence of an adapter ligated to the 5' end. The adapter and any
160 preceding bases are trimmed. Partial matches at the 5' end are allowed.
161 If a `^` character is prepended, the adapter is only found if it is at
162 the beginning of the read. Search in forward read.
163 anywhere_f : List[Str], optional
164 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
165 types of matches as described under `adapter` and `front` are allowed.
166 If the first base of the read is part of the match, the behavior is as
167 with `front`, otherwise as with `adapter`. This option is mostly for
168 rescuing failed library preparations - do not use if you know which end
169 your adapter was ligated to. Search in forward read.
170 adapter_r : List[Str], optional
171 Sequence of an adapter ligated to the 3' end. The adapter and any
172 subsequent bases are trimmed. If a `$` is appended, the adapter is only
173 found if it is at the end of the read. Search in reverse read. If your
174 sequence of interest is "framed" by a 5' and a 3' adapter, use this
175 parameter to define a "linked" primer - see
176 https://cutadapt.readthedocs.io for complete details.
177 front_r : List[Str], optional
178 Sequence of an adapter ligated to the 5' end. The adapter and any
179 preceding bases are trimmed. Partial matches at the 5' end are allowed.
180 If a `^` character is prepended, the adapter is only found if it is at
181 the beginning of the read. Search in reverse read.
182 anywhere_r : List[Str], optional
183 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
184 types of matches as described under `adapter` and `front` are allowed.
185 If the first base of the read is part of the match, the behavior is as
186 with `front`, otherwise as with `adapter`. This option is mostly for
187 rescuing failed library preparations - do not use if you know which end
188 your adapter was ligated to. Search in reverse read.
189 error_rate : Float % Range(0, 1, inclusive_end=True), optional
190 Maximum allowed error rate.
191 indels : Bool, optional
192 Allow insertions or deletions of bases when matching adapters.
193 times : Int % Range(1, None), optional
194 Remove multiple occurrences of an adapter if it is repeated, up to
195 `times` times.
196 overlap : Int % Range(1, None), optional
197 Require at least `overlap` bases of overlap between read and adapter
198 for an adapter to be found.
199 match_read_wildcards : Bool, optional
200 Interpret IUPAC wildcards (e.g., N) in reads.
201 match_adapter_wildcards : Bool, optional
202 Interpret IUPAC wildcards (e.g., N) in adapters.
203 minimum_length : Int % Range(1, None), optional
204 Discard reads shorter than specified value. Note, the cutadapt default
205 of 0 has been overridden, because that value produces empty sequence
206 records.
207 discard_untrimmed : Bool, optional
208 Discard reads in which no adapter was found.
209
210 Returns
211 -------
212 trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
213 The resulting trimmed sequences.
214 ]]></help>
215 <macros>
216 <import>qiime_citation.xml</import>
217 </macros>
218 <expand macro="qiime_citation"/>
219 </tool>