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comparison qiime2/qiime_cutadapt_trim-paired.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_trim-paired" name="qiime cutadapt trim-paired" version="2019.4">
3 <description> - Find and remove adapters in demultiplexed paired-end sequences.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime cutadapt trim-paired
9
10 --i-demultiplexed-sequences=$idemultiplexedsequences
11
12 #set $pcores = '${GALAXY_SLOTS:-4}'
13 #if str($pcores):
14 --p-cores=$pcores
15 #end if
16
17 #if str($padapterf):
18 --p-adapter-f="$padapterf"
19 #end if
20
21 #if str($pfrontf):
22 --p-front-f="$pfrontf"
23 #end if
24
25 #if '__sq__' in str($panywheref):
26 #set $panywheref_temp = $panywheref.replace('__sq__', "'")
27 #set $panywheref = $panywheref_temp
28 #end if
29
30 #if str($panywheref):
31 --p-anywhere-f="$panywheref"
32 #end if
33
34
35 #if str($padapterr):
36 --p-adapter-r="$padapterr"
37 #end if
38
39 #if str($pfrontr):
40 --p-front-r="$pfrontr"
41 #end if
42
43 #if '__sq__' in str($panywherer):
44 #set $panywherer_temp = $panywherer.replace('__sq__', "'")
45 #set $panywherer = $panywherer_temp
46 #end if
47
48 #if str($panywherer):
49 --p-anywhere-r="$panywherer"
50 #end if
51
52 #if $perrorrate:
53 --p-error-rate=$perrorrate
54 #end if
55
56 #if $pnoindels:
57 --p-no-indels
58 #end if
59
60 #if $ptimes:
61 --p-times=$ptimes
62 #end if
63
64 #if $poverlap:
65 --p-overlap=$poverlap
66 #end if
67
68 #if $pmatchreadwildcards:
69 --p-match-read-wildcards
70 #end if
71
72 #if $pnomatchadapterwildcards:
73 --p-no-match-adapter-wildcards
74 #end if
75
76 #if $pminimumlength:
77 --p-minimum-length=$pminimumlength
78 #end if
79
80 #if $pdiscarduntrimmed:
81 --p-discard-untrimmed
82 #end if
83
84 --o-trimmed-sequences=otrimmedsequences
85 ;
86
87 cp otrimmedsequences.qza $otrimmedsequences
88 ]]></command>
89 <inputs>
90 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
91 <param label="--p-adapter-f: TEXT... Sequence of an adapter ligated to the 3' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` 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="True" type="text"/>
92 <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="True" type="text"/>
93 <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="True" type="text"/>
94 <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="True" type="text"/>
95 <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="True" type="text"/>
96 <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="True" type="text"/>
97 <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
98 <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: False]" name="pnoindels" selected="False" type="boolean"/>
99 <param label="--p-times: INTEGER Remove multiple occurrences of an adapter if it is Range(1, None) repeated, up to `times` times. [default: 1]" name="ptimes" optional="True" type="integer" min="1" value="1"/>
100 <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]" name="poverlap" optional="True" type="integer" min="1" value="3"/>
101 <param label="--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"/>
102 <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: False]" name="pnomatchadapterwildcards" selected="False" type="boolean"/>
103 <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]" name="pminimumlength" optional="True" type="integer" min="1" value="1"/>
104 <param label="--p-discard-untrimmed: --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean"/>
105 </inputs>
106 <outputs>
107 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences"/>
108 </outputs>
109 <help><![CDATA[
110 Find and remove adapters in demultiplexed paired-end sequences.
111 ###############################################################
112
113 Search demultiplexed paired-end sequences for adapters and remove them. The
114 parameter descriptions in this method are adapted from the official
115 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
116 for complete details.
117
118 Parameters
119 ----------
120 demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
121 The paired-end sequences to be trimmed.
122 adapter_f : List[Str], optional
123 Sequence of an adapter ligated to the 3' end. The adapter and any
124 subsequent bases are trimmed. If a `$` is appended, the adapter is only
125 found if it is at the end of the read. Search in forward read. If your
126 sequence of interest is "framed" by a 5' and a 3' adapter, use this
127 parameter to define a "linked" primer - see
128 https://cutadapt.readthedocs.io for complete details.
129 front_f : List[Str], optional
130 Sequence of an adapter ligated to the 5' end. The adapter and any
131 preceding bases are trimmed. Partial matches at the 5' end are allowed.
132 If a `^` character is prepended, the adapter is only found if it is at
133 the beginning of the read. Search in forward read.
134 anywhere_f : List[Str], optional
135 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
136 types of matches as described under `adapter` and `front` are allowed.
137 If the first base of the read is part of the match, the behavior is as
138 with `front`, otherwise as with `adapter`. This option is mostly for
139 rescuing failed library preparations - do not use if you know which end
140 your adapter was ligated to. Search in forward read.
141 adapter_r : List[Str], optional
142 Sequence of an adapter ligated to the 3' end. The adapter and any
143 subsequent bases are trimmed. If a `$` is appended, the adapter is only
144 found if it is at the end of the read. Search in reverse read. If your
145 sequence of interest is "framed" by a 5' and a 3' adapter, use this
146 parameter to define a "linked" primer - see
147 https://cutadapt.readthedocs.io for complete details.
148 front_r : List[Str], optional
149 Sequence of an adapter ligated to the 5' end. The adapter and any
150 preceding bases are trimmed. Partial matches at the 5' end are allowed.
151 If a `^` character is prepended, the adapter is only found if it is at
152 the beginning of the read. Search in reverse read.
153 anywhere_r : List[Str], optional
154 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
155 types of matches as described under `adapter` and `front` are allowed.
156 If the first base of the read is part of the match, the behavior is as
157 with `front`, otherwise as with `adapter`. This option is mostly for
158 rescuing failed library preparations - do not use if you know which end
159 your adapter was ligated to. Search in reverse read.
160 error_rate : Float % Range(0, 1, inclusive_end=True), optional
161 Maximum allowed error rate.
162 indels : Bool, optional
163 Allow insertions or deletions of bases when matching adapters.
164 times : Int % Range(1, None), optional
165 Remove multiple occurrences of an adapter if it is repeated, up to
166 `times` times.
167 overlap : Int % Range(1, None), optional
168 Require at least `overlap` bases of overlap between read and adapter
169 for an adapter to be found.
170 match_read_wildcards : Bool, optional
171 Interpret IUPAC wildcards (e.g., N) in reads.
172 match_adapter_wildcards : Bool, optional
173 Interpret IUPAC wildcards (e.g., N) in adapters.
174 minimum_length : Int % Range(1, None), optional
175 Discard reads shorter than specified value. Note, the cutadapt default
176 of 0 has been overridden, because that value produces empty sequence
177 records.
178 discard_untrimmed : Bool, optional
179 Discard reads in which no adapter was found.
180
181 Returns
182 -------
183 trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
184 The resulting trimmed sequences.
185 ]]></help>
186 <macros>
187 <import>qiime_citation.xml</import>
188 </macros>
189 <expand macro="qiime_citation"/>
190 </tool>