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comparison qiime2/qiime_cutadapt_trim-single.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single" version="2019.7"> 2 <tool id="qiime_cutadapt_trim-single" name="qiime cutadapt trim-single"
3 <description> - Find and remove adapters in demultiplexed single-end sequences.</description> 3 version="2020.8">
4 <requirements> 4 <description>Find and remove adapters in demultiplexed single-end sequences.</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime cutadapt trim-single 9 qiime cutadapt trim-single
10
9 --i-demultiplexed-sequences=$idemultiplexedsequences 11 --i-demultiplexed-sequences=$idemultiplexedsequences
10 12
11 #set $pcores = '${GALAXY_SLOTS:-4}'
12 #if str($pcores):
13 --p-cores=$pcores 13 --p-cores=$pcores
14 #end if
15 14
16 15 #if $padapter:
17 #if '__sq__' in str($padapter): 16 --p-adapter
18 #set $padapter_temp = $padapter.replace('__sq__', "'")
19 #set $padapter = $padapter_temp
20 #end if
21
22 #if 'X' in str($padapter):
23 #set $padapter_temp = $padapter.replace('X', "$")
24 #set $padapter = $padapter_temp
25 #end if
26
27 #if str($padapter):
28 --p-adapter="$padapter"
29 #end if
30
31
32
33
34
35 #if '__sq__' in str($pfront):
36 #set $pfront_temp = $pfront.replace('__sq__', "'")
37 #set $pfront = $pfront_temp
38 #end if 17 #end if
39 18
40 #if str($pfront): 19 #if str($pfront):
41 --p-front="$pfront" 20 --p-front=$pfront
42 #end if 21 #end if
43 22 #if '__ob__' in str($panywhere):
44 23 #set $panywhere_temp = $panywhere.replace('__ob__', '[')
45 24 #set $panywhere = $panywhere_temp
46 25 #end if
47 26 #if '__cb__' in str($panywhere):
27 #set $panywhere_temp = $panywhere.replace('__cb__', ']')
28 #set $panywhere = $panywhere_temp
29 #end if
30 #if 'X' in str($panywhere):
31 #set $panywhere_temp = $panywhere.replace('X', '\\')
32 #set $panywhere = $panywhere_temp
33 #end if
48 #if '__sq__' in str($panywhere): 34 #if '__sq__' in str($panywhere):
49 #set $panywhere_temp = $panywhere.replace('__sq__', "'") 35 #set $panywhere_temp = $panywhere.replace('__sq__', "'")
50 #set $panywhere = $panywhere_temp 36 #set $panywhere = $panywhere_temp
51 #end if 37 #end if
38 #if '__db__' in str($panywhere):
39 #set $panywhere_temp = $panywhere.replace('__db__', '"')
40 #set $panywhere = $panywhere_temp
41 #end if
52 42
53 #if str($panywhere): 43 #if str($panywhere):
54 --p-anywhere="$panywhere" 44 --p-anywhere=$panywhere
55 #end if 45 #end if
56 46
57 47 --p-error-rate=$perrorrate
58
59
60 #if str($perrorrate):
61 --p-error-rate=$perrorrate
62 #end if
63 48
64 #if $pnoindels: 49 #if $pnoindels:
65 --p-no-indels 50 --p-no-indels
66 #end if 51 #end if
67 52
68 #if str($ptimes): 53 --p-times=$ptimes
69 --p-times=$ptimes
70 #end if
71 54
72 #if str($poverlap): 55 --p-overlap=$poverlap
73 --p-overlap=$poverlap
74 #end if
75 56
76 #if $pmatchreadwildcards: 57 #if $pmatchreadwildcards:
77 --p-match-read-wildcards 58 --p-match-read-wildcards
78 #end if 59 #end if
79 60
80 #if $pnomatchadapterwildcards: 61 #if $pnomatchadapterwildcards:
81 --p-no-match-adapter-wildcards 62 --p-no-match-adapter-wildcards
82 #end if 63 #end if
83 64
84 #if str($pminimumlength): 65 --p-minimum-length=$pminimumlength
85 --p-minimum-length=$pminimumlength
86 #end if
87 66
88 #if $pdiscarduntrimmed: 67 #if $pdiscarduntrimmed:
89 --p-discard-untrimmed 68 --p-discard-untrimmed
90 #end if 69 #end if
91 70
92 --o-trimmed-sequences=otrimmedsequences 71 --o-trimmed-sequences=otrimmedsequences
93 72
73 #if str($examples) != 'None':
74 --examples=$examples
75 #end if
76
94 ; 77 ;
95 cp otrimmedsequences.qza $otrimmedsequences 78 cp otrimmedsequences.qza $otrimmedsequences
96 ]]></command>
97 <inputs>
98 <param format="qza,no_unzip.zip" label="--i-demultiplexed-sequences: ARTIFACT SampleData[SequencesWithQuality] The single-end sequences to be trimmed. [required]" name="idemultiplexedsequences" optional="False" type="data"/>
99 <param label="--p-adapter: TEXT... Sequence of an adapter ligated to the 3' end. The List[Str] adapter and any subsequent bases are trimmed. If a `$` 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"/>
100 <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"/>
101 <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"/>
102 79
103 <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"/> 80 ]]></command>
104 <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: False]" name="pnoindels" selected="False" type="boolean"/> 81 <inputs>
105 <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"/> 82 <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" />
106 <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"/> 83 <param label="--p-adapter: --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" selected="False" type="boolean" />
107 <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"/> 84 <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="False" type="text" />
108 <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"/> 85 <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="False" type="text" />
109 <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"/> 86 <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) Maximum allowed error rate. [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
110 <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"/> 87 <param label="--p-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: True]" name="pnoindels" selected="False" type="boolean" />
111 </inputs> 88 <param label="--p-times: INTEGER Remove multiple occurrences of an adapter if it is Range(1, None) repeated, up to `times` times. [default: 1]" min="1" name="ptimes" optional="True" type="integer" value="1" />
112 <outputs> 89 <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]" min="1" name="poverlap" optional="True" type="integer" value="3" />
113 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences"/> 90 <param label="--p-match-read-wildcards: --p-match-read-wildcards: / --p-no-match-read-wildcards Interpret IUPAC wildcards (e.g., N) in reads. [default: False]" name="pmatchreadwildcards" selected="False" type="boolean" />
114 </outputs> 91 <param label="--p-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: True]" name="pnomatchadapterwildcards" selected="False" type="boolean" />
115 <help><![CDATA[ 92 <param label="--p-minimum-length: INTEGER Range(1, None) Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
93 <param label="--p-discard-untrimmed: --p-discard-untrimmed: / --p-no-discard-untrimmed Discard reads in which no adapter was found. [default: False]" name="pdiscarduntrimmed" selected="False" type="boolean" />
94 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
95
96 </inputs>
97
98 <outputs>
99 <data format="qza" label="${tool.name} on ${on_string}: trimmedsequences.qza" name="otrimmedsequences" />
100
101 </outputs>
102
103 <help><![CDATA[
116 Find and remove adapters in demultiplexed single-end sequences. 104 Find and remove adapters in demultiplexed single-end sequences.
117 ############################################################### 105 ###############################################################
118 106
119 Search demultiplexed single-end sequences for adapters and remove them. The 107 Search demultiplexed single-end sequences for adapters and remove them. The
120 parameter descriptions in this method are adapted from the official 108 parameter descriptions in this method are adapted from the official
123 111
124 Parameters 112 Parameters
125 ---------- 113 ----------
126 demultiplexed_sequences : SampleData[SequencesWithQuality] 114 demultiplexed_sequences : SampleData[SequencesWithQuality]
127 The single-end sequences to be trimmed. 115 The single-end sequences to be trimmed.
116 cores : Int % Range(1, None), optional
117 Number of CPU cores to use.
128 adapter : List[Str], optional 118 adapter : List[Str], optional
129 Sequence of an adapter ligated to the 3' end. The adapter and any 119 Sequence of an adapter ligated to the 3' end. The adapter and any
130 subsequent bases are trimmed. If a `$` is appended, the adapter is only 120 subsequent bases are trimmed. If a `$` is appended, the adapter is only
131 found if it is at the end of the read. If your sequence of interest is 121 found if it is at the end of the read. If your sequence of interest is
132 "framed" by a 5' and a 3' adapter, use this parameter to define a 122 "framed" by a 5' and a 3' adapter, use this parameter to define a
167 157
168 Returns 158 Returns
169 ------- 159 -------
170 trimmed_sequences : SampleData[SequencesWithQuality] 160 trimmed_sequences : SampleData[SequencesWithQuality]
171 The resulting trimmed sequences. 161 The resulting trimmed sequences.
172 ]]></help> 162 ]]></help>
173 <macros> 163 <macros>
174 <import>qiime_citation.xml</import> 164 <import>qiime_citation.xml</import>
175 </macros> 165 </macros>
176 <expand macro="qiime_citation"/> 166 <expand macro="qiime_citation"/>
177 </tool> 167 </tool>