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comparison qiime2-2020.8/qiime_cutadapt_trim-single.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single"
3 version="2020.8">
4 <description>Find and remove adapters in demultiplexed single-end sequences.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime cutadapt trim-single
10
11 --i-demultiplexed-sequences=$idemultiplexedsequences
12
13 --p-cores=$pcores
14
15 #if $padapter:
16 --p-adapter
17 #end if
18
19 #if str($pfront):
20 --p-front=$pfront
21 #end if
22 #if '__ob__' in str($panywhere):
23 #set $panywhere_temp = $panywhere.replace('__ob__', '[')
24 #set $panywhere = $panywhere_temp
25 #end if
26 #if '__cb__' in str($panywhere):
27 #set $panywhere_temp = $panywhere.replace('__cb__', ']')
28 #set $panywhere = $panywhere_temp
29 #end if
30 #if 'X' in str($panywhere):
31 #set $panywhere_temp = $panywhere.replace('X', '\\')
32 #set $panywhere = $panywhere_temp
33 #end if
34 #if '__sq__' in str($panywhere):
35 #set $panywhere_temp = $panywhere.replace('__sq__', "'")
36 #set $panywhere = $panywhere_temp
37 #end if
38 #if '__db__' in str($panywhere):
39 #set $panywhere_temp = $panywhere.replace('__db__', '"')
40 #set $panywhere = $panywhere_temp
41 #end if
42
43 #if str($panywhere):
44 --p-anywhere=$panywhere
45 #end if
46
47 --p-error-rate=$perrorrate
48
49 #if $pnoindels:
50 --p-no-indels
51 #end if
52
53 --p-times=$ptimes
54
55 --p-overlap=$poverlap
56
57 #if $pmatchreadwildcards:
58 --p-match-read-wildcards
59 #end if
60
61 #if $pnomatchadapterwildcards:
62 --p-no-match-adapter-wildcards
63 #end if
64
65 --p-minimum-length=$pminimumlength
66
67 #if $pdiscarduntrimmed:
68 --p-discard-untrimmed
69 #end if
70
71 --o-trimmed-sequences=otrimmedsequences
72
73 #if str($examples) != 'None':
74 --examples=$examples
75 #end if
76
77 ;
78 cp otrimmedsequences.qza $otrimmedsequences
79
80 ]]></command>
81 <inputs>
82 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality] The single-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data" />
83 <param label="--p-adapter: --p-adapter: TEXT... Sequence of an adapter ligated to the 3\' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. 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="padapter" selected="False" type="boolean" />
84 <param label="--p-front: 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. [optional]" name="pfront" optional="False" type="text" />
85 <param label="--p-anywhere: TEXT... Sequence of an adapter that may be ligated to the 5\' List[Str] 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. [optional]" name="panywhere" optional="False" type="text" />
86 <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" />
87 <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: True]" name="pnoindels" selected="False" type="boolean" />
88 <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" />
89 <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" />
90 <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" />
91 <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" />
92 <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" />
93 <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" />
94 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
95
96 </inputs>
97
98 <outputs>
99 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences" />
100
101 </outputs>
102
103 <help><![CDATA[
104 Find and remove adapters in demultiplexed single-end sequences.
105 ###############################################################
106
107 Search demultiplexed single-end sequences for adapters and remove them. The
108 parameter descriptions in this method are adapted from the official
109 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
110 for complete details.
111
112 Parameters
113 ----------
114 demultiplexed_sequences : SampleData[SequencesWithQuality]
115 The single-end sequences to be trimmed.
116 cores : Int % Range(1, None), optional
117 Number of CPU cores to use.
118 adapter : List[Str], optional
119 Sequence of an adapter ligated to the 3' end. The adapter and any
120 subsequent bases are trimmed. If a `$` is appended, the adapter is only
121 found if it is at the end of the read. If your sequence of interest is
122 "framed" by a 5' and a 3' adapter, use this parameter to define a
123 "linked" primer - see https://cutadapt.readthedocs.io for complete
124 details.
125 front : List[Str], optional
126 Sequence of an adapter ligated to the 5' end. The adapter and any
127 preceding bases are trimmed. Partial matches at the 5' end are allowed.
128 If a `^` character is prepended, the adapter is only found if it is at
129 the beginning of the read.
130 anywhere : List[Str], optional
131 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
132 types of matches as described under `adapter` and `front` are allowed.
133 If the first base of the read is part of the match, the behavior is as
134 with `front`, otherwise as with `adapter`. This option is mostly for
135 rescuing failed library preparations - do not use if you know which end
136 your adapter was ligated to.
137 error_rate : Float % Range(0, 1, inclusive_end=True), optional
138 Maximum allowed error rate.
139 indels : Bool, optional
140 Allow insertions or deletions of bases when matching adapters.
141 times : Int % Range(1, None), optional
142 Remove multiple occurrences of an adapter if it is repeated, up to
143 `times` times.
144 overlap : Int % Range(1, None), optional
145 Require at least `overlap` bases of overlap between read and adapter
146 for an adapter to be found.
147 match_read_wildcards : Bool, optional
148 Interpret IUPAC wildcards (e.g., N) in reads.
149 match_adapter_wildcards : Bool, optional
150 Interpret IUPAC wildcards (e.g., N) in adapters.
151 minimum_length : Int % Range(1, None), optional
152 Discard reads shorter than specified value. Note, the cutadapt default
153 of 0 has been overridden, because that value produces empty sequence
154 records.
155 discard_untrimmed : Bool, optional
156 Discard reads in which no adapter was found.
157
158 Returns
159 -------
160 trimmed_sequences : SampleData[SequencesWithQuality]
161 The resulting trimmed sequences.
162 ]]></help>
163 <macros>
164 <import>qiime_citation.xml</import>
165 </macros>
166 <expand macro="qiime_citation"/>
167 </tool>