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comparison qiime_cutadapt_trim-single.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single" version="2018.4">
3 <description> - Find and remove adapters in demultiplexed single-end sequences.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8
9 qiime cutadapt trim-single --i-demultiplexed-sequences=$idemultiplexedsequences
10
11 #if '__sq__' in str($panywhere):
12 #set $panywhere_temp = $panywhere.replace('__sq__', "'")
13 #set $panywhere = $panywhere_temp
14 #end if
15
16 #if str($panywhere):
17 --p-anywhere="$panywhere"
18 #end if
19
20
21 #if str($cmdconfig) != 'None':
22 --cmd-config=$cmdconfig
23 #end if
24
25 #if $poverlap:
26 --p-overlap=$poverlap
27 #end if
28
29 #if str($pfront):
30 --p-front="$pfront"
31 #end if
32
33 #if $ptimes:
34 --p-times=$ptimes
35 #end if
36
37 --o-trimmed-sequences=otrimmedsequences
38
39 #if $pindels:
40 --p-indels
41 #end if
42
43 #if $perrorrate:
44 --p-error-rate=$perrorrate
45 #end if
46
47 #if $pmatchadapterwildcards:
48 --p-match-adapter-wildcards
49 #end if
50
51 #set $slots = '${GALAXY_SLOTS:-4}'
52 --p-cores=$slots
53
54 #if str($padapter):
55 --p-adapter="$padapter"
56 #end if
57
58 #if $pmatchreadwildcards:
59 --p-match-read-wildcards
60 #end if
61 ;
62 cp otrimmedsequences.qza $otrimmedsequences
63
64 ]]></command>
65 <inputs>
66 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: SampleData[SequencesWithQuality] The single-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
67
68 <param label="--p-adapter: Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. 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"/>
69
70 <param label="--p-front: 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. [optional]" name="pfront" optional="True" type="text"/>
71 <param label="--p-anywhere: 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. [optional]" name="panywhere" optional="True" type="text"/>
72
73 <param label="--p-error-rate: Maximum allowed error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" value="0.1"/>
74
75 <param label="--p-indels: --p-no-indels Allow insertions or deletions of bases when matching adapters. [default: True]" name="pindels" checked="False" type="boolean"/>
76 <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"/>
77
78 <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"/>
79
80 <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"/>
81 <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"/>
82
83 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
84 </inputs>
85 <outputs>
86 <data format="qza" label="${tool.name} on ${on_string}: trimmed-sequences.qza" name="otrimmedsequences"/>
87 </outputs>
88 <help><![CDATA[
89 Find and remove adapters in demultiplexed single-end sequences.
90 ----------------------------------------------------------------
91
92 Search demultiplexed single-end sequences for adapters and remove them. The
93 parameter descriptions in this method are adapted from the official
94 cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
95 for complete details.
96
97 Parameters
98 ----------
99 demultiplexed_sequences : SampleData[SequencesWithQuality]
100 The single-end sequences to be trimmed.
101 adapter : List[Str], optional
102 Sequence of an adapter ligated to the 3' end. The adapter and any
103 subsequent bases are trimmed. If a `$` is appended, the adapter is only
104 found if it is at the end of the read. If your sequence of interest is
105 "framed" by a 5' and a 3' adapter, use this parameter to define a
106 "linked" primer - see https://cutadapt.readthedocs.io for complete
107 details.
108 front : List[Str], optional
109 Sequence of an adapter ligated to the 5' end. The adapter and any
110 preceding bases are trimmed. Partial matches at the 5' end are allowed.
111 If a `^` character is prepended, the adapter is only found if it is at
112 the beginning of the read.
113 anywhere : List[Str], optional
114 Sequence of an adapter that may be ligated to the 5' or 3' end. Both
115 types of matches as described under `adapter` and `front` are allowed.
116 If the first base of the read is part of the match, the behavior is as
117 with `front`, otherwise as with `adapter`. This option is mostly for
118 rescuing failed library preparations - do not use if you know which end
119 your adapter was ligated to.
120 error_rate : Float % Range(0, 1, inclusive_end=True), optional
121 Maximum allowed error rate.
122 indels : Bool, optional
123 Allow insertions or deletions of bases when matching adapters.
124 times : Int % Range(1, None), optional
125 Remove multiple occurrences of an adapter if it is repeated, up to
126 `times` times.
127 overlap : Int % Range(1, None), optional
128 Require at least `overlap` bases of overlap between read and adapter
129 for an adapter to be found.
130 match_read_wildcards : Bool, optional
131 Interpret IUPAC wildcards (e.g., N) in reads.
132 match_adapter_wildcards : Bool, optional
133 Interpret IUPAC wildcards (e.g., N) in adapters.
134
135 Returns
136 -------
137 trimmed_sequences : SampleData[SequencesWithQuality]
138 The resulting trimmed sequences.
139 ]]>
140 </help>
141 </tool>