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

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single" version="2019.4">
3 <description> - Find and remove adapters in demultiplexed single-end sequences.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime cutadapt trim-single
9 --i-demultiplexed-sequences=$idemultiplexedsequences
10
11 #set $pcores = '${GALAXY_SLOTS:-4}'
12 #if str($pcores):
13 --p-cores=$pcores
14 #end if
15
16 #if str($padapter):
17 --p-adapter="$padapter"
18 #end if
19
20 #if str($pfront):
21 --p-front="$pfront"
22 #end if
23
24 #if '__sq__' in str($panywhere):
25 #set $panywhere_temp = $panywhere.replace('__sq__', "'")
26 #set $panywhere = $panywhere_temp
27 #end if
28
29 #if str($panywhere):
30 --p-anywhere="$panywhere"
31 #end if
32
33
34 #if $perrorrate:
35 --p-error-rate=$perrorrate
36 #end if
37
38 #if $pnoindels:
39 --p-no-indels
40 #end if
41
42 #if $ptimes:
43 --p-times=$ptimes
44 #end if
45
46 #if $poverlap:
47 --p-overlap=$poverlap
48 #end if
49
50 #if $pmatchreadwildcards:
51 --p-match-read-wildcards
52 #end if
53
54 #if $pnomatchadapterwildcards:
55 --p-no-match-adapter-wildcards
56 #end if
57
58 #if $pminimumlength:
59 --p-minimum-length=$pminimumlength
60 #end if
61
62 #if $pdiscarduntrimmed:
63 --p-discard-untrimmed
64 #end if
65
66 --o-trimmed-sequences=otrimmedsequences
67
68 ;
69 cp otrimmedsequences.qza $otrimmedsequences
70 ]]></command>
71 <inputs>
72 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality] The single-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
73 <param label="--p-adapter: TEXT... Sequence of an adapter ligated to the 3' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` 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" optional="True" type="text"/>
74 <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="True" type="text"/>
75 <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="True" type="text"/>
76
77 <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"/>
78 <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: False]" name="pnoindels" selected="False" type="boolean"/>
79 <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"/>
80 <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"/>
81 <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"/>
82 <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"/>
83 <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"/>
84 <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"/>
85 </inputs>
86 <outputs>
87 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences"/>
88 </outputs>
89 <help><![CDATA[
90 Find and remove adapters in demultiplexed single-end sequences.
91 ###############################################################
92
93 Search demultiplexed single-end sequences for adapters and remove them. The
94 parameter descriptions in this method are adapted from the official
95 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
96 for complete details.
97
98 Parameters
99 ----------
100 demultiplexed_sequences : SampleData[SequencesWithQuality]
101 The single-end sequences to be trimmed.
102 adapter : List[Str], optional
103 Sequence of an adapter ligated to the 3' end. The adapter and any
104 subsequent bases are trimmed. If a `$` is appended, the adapter is only
105 found if it is at the end of the read. If your sequence of interest is
106 "framed" by a 5' and a 3' adapter, use this parameter to define a
107 "linked" primer - see https://cutadapt.readthedocs.io for complete
108 details.
109 front : List[Str], optional
110 Sequence of an adapter ligated to the 5' end. The adapter and any
111 preceding bases are trimmed. Partial matches at the 5' end are allowed.
112 If a `^` character is prepended, the adapter is only found if it is at
113 the beginning of the read.
114 anywhere : List[Str], optional
115 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
116 types of matches as described under `adapter` and `front` are allowed.
117 If the first base of the read is part of the match, the behavior is as
118 with `front`, otherwise as with `adapter`. This option is mostly for
119 rescuing failed library preparations - do not use if you know which end
120 your adapter was ligated to.
121 error_rate : Float % Range(0, 1, inclusive_end=True), optional
122 Maximum allowed error rate.
123 indels : Bool, optional
124 Allow insertions or deletions of bases when matching adapters.
125 times : Int % Range(1, None), optional
126 Remove multiple occurrences of an adapter if it is repeated, up to
127 `times` times.
128 overlap : Int % Range(1, None), optional
129 Require at least `overlap` bases of overlap between read and adapter
130 for an adapter to be found.
131 match_read_wildcards : Bool, optional
132 Interpret IUPAC wildcards (e.g., N) in reads.
133 match_adapter_wildcards : Bool, optional
134 Interpret IUPAC wildcards (e.g., N) in adapters.
135 minimum_length : Int % Range(1, None), optional
136 Discard reads shorter than specified value. Note, the cutadapt default
137 of 0 has been overridden, because that value produces empty sequence
138 records.
139 discard_untrimmed : Bool, optional
140 Discard reads in which no adapter was found.
141
142 Returns
143 -------
144 trimmed_sequences : SampleData[SequencesWithQuality]
145 The resulting trimmed sequences.
146 ]]></help>
147 <macros>
148 <import>qiime_citation.xml</import>
149 </macros>
150 <expand macro="qiime_citation"/>
151 </tool>