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comparison qiime2/qiime_cutadapt_trim-paired.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired" version="2018.4">
3 <description> - Find and remove adapters in demultiplexed paired-end sequences.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8
9 qiime cutadapt trim-paired --i-demultiplexed-sequences=$idemultiplexedsequences
10
11 #if str($padapterf):
12 --p-adapter-f="$padapterf"
13 #end if
14
15 --o-trimmed-sequences=otrimmedsequences
16
17 #if str($cmdconfig) != 'None':
18 --cmd-config=$cmdconfig
19 #end if
20
21 #if '__sq__' in str($panywheref):
22 #set $panywheref_temp = $panywheref.replace('__sq__', "'")
23 #set $panywheref = $panywheref_temp
24 #end if
25
26 #if str($panywheref):
27 --p-anywhere-f="$panywheref"
28 #end if
29
30 #if $poverlap:
31 --p-overlap=$poverlap
32 #end if
33
34 #if '__sq__' in str($panywherer):
35 #set $panywherer_temp = $panywherer.replace('__sq__', "'")
36 #set $panywherer = $panywherer_temp
37 #end if
38
39 #if str($panywherer):
40 --p-anywhere-r="$panywherer"
41 #end if
42
43 #if $ptimes:
44 --p-times=$ptimes
45 #end if
46
47 #if $pindels:
48 --p-indels
49 #end if
50
51 #if str($padapterr):
52 --p-adapter-r="$padapterr"
53 #end if
54
55 #if $perrorrate:
56 --p-error-rate=$perrorrate
57 #end if
58
59 #if $pmatchadapterwildcards:
60 --p-match-adapter-wildcards
61 #end if
62
63 #set $slots = '${GALAXY_SLOTS:-4}'
64 --p-cores=$slots
65
66 #if str($pfrontr):
67 --p-front-r="$pfrontr"
68 #end if
69
70 #if str($pfrontf):
71 --p-front-f="$pfrontf"
72 #end if
73
74 #if $pmatchreadwildcards:
75 --p-match-read-wildcards
76 #end if
77 ;
78
79 cp otrimmedsequences.qza $otrimmedsequences
80
81 ]]></command>
82 <inputs>
83 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
84
85 <param label="--p-adapter-f: Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` 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="True" type="text"/>
86 <param label="--p-front-f: Sequence of an adapter ligated to the 5' end. The 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="True" type="text"/>
87 <param label="--p-anywhere-f: Sequence of an adapter that may be ligated to the 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="True" type="text"/>
88
89 <param label="--p-adapter-r: Sequence of an adapter ligated to the 3' end. The 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="True" type="text"/>
90 <param label="--p-front-r: Sequence of an adapter ligated to the 5' end. The 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="True" type="text"/>
91 <param label="--p-anywhere-r: Sequence of an adapter that may be ligated to the 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="True" type="text"/>
92
93 <param label="--p-error-rate: Maximum allowed error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" value="0.1"/>
94
95 <param label="--p-indels: --p-no-indels Allow insertions or deletions of bases when matching adapters. [default: True]" name="pindels" checked="False" type="boolean"/>
96
97 <param label="--p-times: Remove multiple occurrences of an adapter if it is repeated, up to `times` times. [default: 1]" name="ptimes" optional="True" type="integer" value="1"/>
98
99 <param label="--p-overlap: Require at least `overlap` bases of overlap between read and adapter for an adapter to be found. [default: 3]" name="poverlap" optional="True" type="integer" value="3"/>
100
101 <param label="--p-match-read-wildcards: --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" checked="False" type="boolean"/>
102
103 <param label="--p-match-adapter-wildcards: --p-no-match-adapter-wildcards Interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pmatchadapterwildcards" checked="False" type="boolean"/>
104
105 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
106 </inputs>
107 <outputs>
108 <data format="qza" label="${tool.name} on ${on_string}: trimmed-sequences.qza" name="otrimmedsequences"/>
109 </outputs>
110 <help><![CDATA[
111 Find and remove adapters in demultiplexed paired-end sequences.
112 ----------------------------------------------------------------
113
114 Search demultiplexed paired-end sequences for adapters and remove them. The
115 parameter descriptions in this method are adapted from the official
116 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
117 for complete details.
118
119 Parameters
120 ----------
121 demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
122 The paired-end sequences to be trimmed.
123 adapter_f : List[Str], optional
124 Sequence of an adapter ligated to the 3' end. The adapter and any
125 subsequent bases are trimmed. If a `$` is appended, the adapter is only
126 found if it is at the end of the read. Search in forward read. If your
127 sequence of interest is "framed" by a 5' and a 3' adapter, use this
128 parameter to define a "linked" primer - see
129 https://cutadapt.readthedocs.io for complete details.
130 front_f : List[Str], optional
131 Sequence of an adapter ligated to the 5' end. The adapter and any
132 preceding bases are trimmed. Partial matches at the 5' end are allowed.
133 If a `^` character is prepended, the adapter is only found if it is at
134 the beginning of the read. Search in forward read.
135 anywhere_f : List[Str], optional
136 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
137 types of matches as described under `adapter` and `front` are allowed.
138 If the first base of the read is part of the match, the behavior is as
139 with `front`, otherwise as with `adapter`. This option is mostly for
140 rescuing failed library preparations - do not use if you know which end
141 your adapter was ligated to. Search in forward read.
142 adapter_r : List[Str], optional
143 Sequence of an adapter ligated to the 3' end. The adapter and any
144 subsequent bases are trimmed. If a `$` is appended, the adapter is only
145 found if it is at the end of the read. Search in reverse read. If your
146 sequence of interest is "framed" by a 5' and a 3' adapter, use this
147 parameter to define a "linked" primer - see
148 https://cutadapt.readthedocs.io for complete details.
149 front_r : List[Str], optional
150 Sequence of an adapter ligated to the 5' end. The adapter and any
151 preceding bases are trimmed. Partial matches at the 5' end are allowed.
152 If a `^` character is prepended, the adapter is only found if it is at
153 the beginning of the read. Search in reverse read.
154 anywhere_r : List[Str], optional
155 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
156 types of matches as described under `adapter` and `front` are allowed.
157 If the first base of the read is part of the match, the behavior is as
158 with `front`, otherwise as with `adapter`. This option is mostly for
159 rescuing failed library preparations - do not use if you know which end
160 your adapter was ligated to. Search in reverse read.
161 error_rate : Float % Range(0, 1, inclusive_end=True), optional
162 Maximum allowed error rate.
163 indels : Bool, optional
164 Allow insertions or deletions of bases when matching adapters.
165 times : Int % Range(1, None), optional
166 Remove multiple occurrences of an adapter if it is repeated, up to
167 `times` times.
168 overlap : Int % Range(1, None), optional
169 Require at least `overlap` bases of overlap between read and adapter
170 for an adapter to be found.
171 match_read_wildcards : Bool, optional
172 Interpret IUPAC wildcards (e.g., N) in reads.
173 match_adapter_wildcards : Bool, optional
174 Interpret IUPAC wildcards (e.g., N) in adapters.
175
176 Returns
177 -------
178 trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
179 The resulting trimmed sequences.
180 ]]>
181 </help>
182 <macros>
183 <import>qiime_citation.xml</import>
184 </macros>
185 <expand macro="qiime_citation" />
186 </tool>