Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_cutadapt_trim-single.xml @ 0:370e0b6e9826 draft
Uploaded
author | florianbegusch |
---|---|
date | Wed, 17 Jul 2019 03:05:17 -0400 |
parents | |
children | 914fa4daf16a |
comparison
equal
deleted
inserted
replaced
-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> |